XCMS Parameter Optimization with IPO

Gunnar Libiseller, Thomas Riebenbauer
JOANNEUM RESEARCH Forschungsgesellschaft m.b.H., Graz, Austria

2016-10-17

Introduction

This document describes how to use the R-package ‘IPO’ to optimize ‘xcms’ parameters. Code examples on how to use ‘IPO’ are provided. Additional to ‘IPO’ the R-packages ‘xcms’ and ‘rsm’ are required. The R-package ‘msdata’ and’mtbls2’ are recommended. The optimization process looks as following:


IPO optimization process

Installation

# try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("IPO")

Installing main suggested packages

# for examples of peak picking parameter optimization:
biocLite("msdata")
# for examples of optimization of retention time correction and grouping
# parameters:
biocLite("faahKO")

Raw data

‘xcms’ handles the file processing hence all files can be used that can be processed by ‘xcms’.

datapath <- system.file("cdf", package = "faahKO")
datafiles <- list.files(datapath, recursive = TRUE, full.names=TRUE)

Optimize peak picking parameters

To optimize parameters different values (levels) have to tested for these parameters. To efficiently test many different levels design of experiment (DoE) is used. Box-Behnken and central composite designs set three evenly spaced levels for each parameter. The method ‘getDefaultXcmsSetStartingParams’ provides default values for the lower and upper levels defining a range. Since the levels are evenly spaced the middle level or center point is calculated automatically. To edit the starting levels of a parameter set the lower and upper level as desired. If a parameter should not be optimized, set a single default value for ‘xcms’ processing, do not set this parameter to NULL.

The method ‘getDefaultXcmsSetStartingParams’ creates a list with default values for the optimization of the peak picking methods ‘centWave’ or ‘matchedFilter’. To choose between these two method set the parameter accordingly.

The method ‘optimizeXcmsSet’ has the following parameters: - files: the raw data which is the basis for optimization. This does not necessarly need to be the whole dataset, only quality controls should suffice. - params: a list consisting of items named according to ‘xcms’ peak picking methods parameters. A default list is created by ‘getDefaultXcmsSetStartingParams’. - nSlaves: the number ofexperiments of an DoE processed in parallel - subdir: a directory where the response surface models are stored. Can also be NULL if no rsm’s should be saved.

The optimization process starts at the specified levels. After the calculation of the DoE is finished the result is evaluated and the levels automatically set accordingly. Then a new DoE is generated and processed. This continues until an optimum is found.

The result of peak picking optimization is a list consisting of all calculated DoEs including the used levels, design, response, rsm and best setting. Additionally the last list item is a list (‘$best_settings’) providing the optimized parameters (‘$parameters’), an xcmsSet object (‘$xset’) calculated with these parameters and the response this ‘xcms’-object gives.

library(IPO)
peakpickingParameters <- getDefaultXcmsSetStartingParams('matchedFilter')
#setting levels for step to 0.2 and 0.3 (hence 0.25 is the center point)
peakpickingParameters$step <- c(0.2, 0.3)
peakpickingParameters$fwhm <- c(40, 50)
#setting only one value for steps therefore this parameter is not optimized
peakpickingParameters$steps <- 2

time.xcmsSet <- system.time({ # measuring time
resultPeakpicking <- 
  optimizeXcmsSet(files = datafiles[1:2], 
                  params = peakpickingParameters, 
                  nSlaves = 1, 
                  subdir = "rsmDirectory")
})
#> 
#> starting new DoE with:
#> fwhm: c(40, 50)
#> snthresh: c(3, 17)
#> step: c(0.2, 0.3)
#> steps: 2
#> sigma: 0
#> max: 5
#> mzdiff: 0
#> index: FALSE
#> nSlaves: 1
#> 1
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:659 400:1525 500:2362 600:3329
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:583 400:1342 500:2054 600:2997
#> 2
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:561 400:1298 500:1978 600:2871
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:651 400:1492 500:2325 600:3248
#> 3
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:82 400:246 500:403 600:659
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:60 400:225 500:352 600:526
#> 4
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:64 400:235 500:368 600:548
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:89 400:264 500:445 600:700
#> 5
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:880 500:1885
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:1039 500:2213
#> 6
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:858 500:1839
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:1048 500:2199
#> 7
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:147 500:354
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:177 500:418
#> 8
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:152 500:372
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:190 500:461
#> 9
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:178 450:475 575:840
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:237 450:595 575:1085
#> 10
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:229 450:581 575:1064
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:179 450:475 575:845
#> 11
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:179 450:475 575:834
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:242 450:603 575:1103
#> 12
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:807 450:1858 575:2971
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:677 450:1558 575:2551
#> 13
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:111 450:286 575:499
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:137 450:341 575:642
#> 14
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:138 400:439 500:731 600:1115
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 300:114 400:359 500:572 600:894
#> 15
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:238 500:583
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 350:302 500:739
#> 16
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:178 450:475 575:840
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 325:237 450:595 575:1085
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:699 445:1528 567:2469
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:814 445:1806 567:2859
#> 
#> starting new DoE with:
#> fwhm: c(45, 55)
#> snthresh: c(1, 15)
#> step: c(0.205, 0.285)
#> steps: 2
#> sigma: 0
#> max: 5
#> mzdiff: 0
#> index: FALSE
#> nSlaves: 1
#> 1
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:1295 405:2648 507:4028
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:1369 405:2746 507:4137
#> 2
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:1247 405:2510 507:3834
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:1204 405:2466 507:3705
#> 3
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:83 405:259 507:423
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:110 405:318 507:532
#> 4
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:113 405:330 507:545
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:85 405:269 507:435
#> 5
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:1712 484:3390
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:1721 484:3388
#> 6
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:1576 484:3157
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:1620 484:3248
#> 7
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:152 484:382
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:194 484:475
#> 8
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:199 484:490
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:156 484:397
#> 9
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:298 445:734 567:1260
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:223 445:578 567:992
#> 10
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:287 445:718 567:1237
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:224 445:575 567:989
#> 11
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:220 445:575 567:986
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:301 445:752 567:1281
#> 12
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:1471 445:3013 567:4499
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:1456 445:2921 567:4447
#> 13
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:152 445:405 567:709
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:121 445:335 567:561
#> 14
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:162 405:473 507:756
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:212 405:601 507:976
#> 15
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:279 484:682
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 342:368 484:878
#> 16
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:223 445:578 567:992
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 322:298 445:734 567:1260
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:1247 405:2510 507:3834
#> Loading required package: xcms
#> Loading required package: mzR
#> Loading required package: Rcpp
#> Loading required package: BiocGenerics
#> Loading required package: parallel
#> 
#> Attaching package: 'BiocGenerics'
#> 
#> The following objects are masked from 'package:parallel':
#> 
#>     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
#>     clusterExport, clusterMap, parApply, parCapply, parLapply,
#>     parLapplyLB, parRapply, parSapply, parSapplyLB
#> 
#> The following objects are masked from 'package:stats':
#> 
#>     IQR, mad, xtabs
#> 
#> The following objects are masked from 'package:base':
#> 
#>     Filter, Find, Map, Position, Reduce, anyDuplicated, append,
#>     as.data.frame, cbind, colnames, do.call, duplicated, eval, evalq,
#>     get, grep, grepl, intersect, is.unsorted, lapply, lengths, mapply,
#>     match, mget, order, paste, pmax, pmax.int, pmin, pmin.int, rank,
#>     rbind, rownames, sapply, setdiff, sort, table, tapply, union,
#>     unique, unsplit, which, which.max, which.min
#> 
#> Loading required package: ProtGenerics
#> Loading required package: Biobase
#> Welcome to Bioconductor
#> 
#>     Vignettes contain introductory material; view with
#>     'browseVignettes()'. To cite Bioconductor, see
#>     'citation("Biobase")', and for packages 'citation("pkgname")'.
#> 
#> 302:1204 405:2466 507:3705
#> no increase, stopping
#> best parameter settings:
#> fwhm: 50
#> snthresh: 3
#> step: 0.245
#> steps: 2
#> sigma: 21.2332257516562
#> max: 5
#> mzdiff: 0.31
#> index: FALSE
#> nSlaves: 1
resultPeakpicking$best_settings$result
#>    ExpId   #peaks   #NonRP      #RP      PPS 
#>    0.000 3260.000 2272.000  573.000  144.511
optimizedXcmsSetObject <- resultPeakpicking$best_settings$xset

The response surface models of all optimization steps for the parameter optimization of peak picking look as following:


Response surface models of DoE 1 of peak picking parameter optimization


Response surface models of DoE 2 of peak picking parameter optimization

Currently the ‘xcms’ peak picking methods ‘centWave’ and ‘matchedFilter’ are supported. The parameter ‘peakwidth’ of the peak picking method ‘centWave’ needs two values defining a minimum and maximum peakwidth. These two values need separate optimization and are therefore split into ‘min_peakwidth’ and ‘max_peakwidth’ in ‘getDefaultXcmsSetStartingParams’. Also for the ‘centWave’ parameter prefilter two values have to be set. To optimize these use set ‘prefilter’ to optimize the first value and ‘prefilter_value’ to optimize the second value respectively.

Optimize retention time correction and grouping parameters

Optimization of retention time correction and grouping parameters is done simultaneously. The method ‘getDefaultRetGroupStartingParams’ provides default optimization levels for the ‘xcms’ retention time correction method ‘obiwarp’ and the grouping method ‘density’. Modifying these levels should be done the same way done for the peak picking parameter optimization.

The method ‘getDefaultRetGroupStartingParams’ only supports one retention time correction method (‘obiwarp’) and one grouping method (‘density’) at the moment.

The method ‘optimizeRetGroup’ provides the following parameter: - xset: an ‘xcmsSet’-object used as basis for retention time correction and grouping. - params: a list consisting of items named according to ‘xcms’ retention time correction and grouping methods parameters. A default list is created by ‘getDefaultRetGroupStartingParams’. - nSlaves: the number ofexperiments of an DoE processed in parallel - subdir: a directory where the response surface models are stored. Can also be NULL if no rsm’s should be saved.

A list is returned similar to the one returned from peak picking optimization. The last list item consists of the optimized retention time correction and grouping parameters (‘$best_settings’).

retcorGroupParameters <- getDefaultRetGroupStartingParams()
retcorGroupParameters$profStep <- 1
retcorGroupParameters$gapExtend <- 2.7
time.RetGroup <- system.time({ # measuring time
resultRetcorGroup <-
  optimizeRetGroup(xset = optimizedXcmsSetObject, 
                   params = retcorGroupParameters, 
                   nSlaves = 1, 
                   subdir = "rsmDirectory")
})
#> 
#> starting new DoE with:
#> distFunc: cor_opt
#> gapInit: c(0, 0.4)
#> gapExtend: 2.7
#> profStep: 1
#> plottype: none
#> response: 1
#> factorDiag: 2
#> factorGap: 1
#> localAlignment: 0
#> retcorMethod: obiwarp
#> bw: c(22, 38)
#> minfrac: c(0.3, 0.7)
#> mzwid: c(0.015, 0.035)
#> minsamp: 1
#> max: 50
#> center: 2
#> 
#> starting new DoE with:
#> gapInit: c(0.16, 0.64)
#> bw: c(12.4, 31.6)
#> minfrac: c(0.46, 0.94)
#> mzwid: c(0.023, 0.047)
#> distFunc: cor_opt
#> gapExtend: 2.7
#> profStep: 1
#> plottype: none
#> response: 1
#> factorDiag: 2
#> factorGap: 1
#> localAlignment: 0
#> retcorMethod: obiwarp
#> minsamp: 1
#> max: 50
#> center: 2
#> profStep or minfrac greater 1, decreasing to 0.54 and 1
#> 
#> starting new DoE with:
#> gapInit: c(0.304, 0.784)
#> bw: c(0.879999999999999, 23.92)
#> minfrac: c(0.54, 1)
#> mzwid: c(0.0326, 0.0614)
#> distFunc: cor_opt
#> gapExtend: 2.7
#> profStep: 1
#> plottype: none
#> response: 1
#> factorDiag: 2
#> factorGap: 1
#> localAlignment: 0
#> retcorMethod: obiwarp
#> minsamp: 1
#> max: 50
#> center: 2
#> no increase stopping

The response surface models of all optimization steps for the retention time correction and grouping parameters look as following:


Response surface models of DoE 1 of retention time correction and grouping parameter optimization


Response surface models of DoE 2 of retention time correction and grouping parameter optimizationn


Response surface models of DoE 3 of retention time correction and grouping parameter optimization

Currently the ‘xcms’ retention time correction method ‘obiwarp’ and grouping method ‘density’ are supported.

Display optimized settings

A script which you can use to process your raw data can be generated by using the function ‘writeRScript’.

writeRScript(resultPeakpicking$best_settings$parameters, 
             resultRetcorGroup$best_settings, 
             nSlaves=1)
#> library(xcms)
#> library(Rmpi)
#> xset <- xcmsSet(method="matchedFilter", fwhm=50, snthresh=3, step=0.245, steps=2, sigma=21.2332257516562, max=5, mzdiff=0.31, index=FALSE, nSlaves=1)
#> xset <- retcor(xset, method="obiwarp",
#>                   plottype="none", distFunc="cor_opt", profStep=1, center=2, response=1, gapInit=0.544, gapExtend=2.7, factorDiag=2, factorGap=1, localAlignment=0)
#> xset <- group(xset, method="density", 
#>                 bw=12.4, mzwid=0.047, minfrac=0.94, minsamp=1, max=50)
#> xset <- fillPeaks(xset, nSlaves=1)

Running times and session info

Above calculations proceeded with following running times.

time.xcmsSet # time for optimizing peak picking parameters
#>    user  system elapsed 
#>    6.97    0.22  232.47
time.RetGroup # time for optimizing retention time correction and grouping parameters
#>    user  system elapsed 
#>  343.67    5.20  348.95

sessionInfo()
#> R version 3.3.1 (2016-06-21)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows Server 2012 R2 x64 (build 9600)
#> 
#> locale:
#> [1] LC_COLLATE=C                          
#> [2] LC_CTYPE=English_United States.1252   
#> [3] LC_MONETARY=English_United States.1252
#> [4] LC_NUMERIC=C                          
#> [5] LC_TIME=English_United States.1252    
#> 
#> attached base packages:
#> [1] parallel  stats     graphics  grDevices utils     datasets  methods  
#> [8] base     
#> 
#> other attached packages:
#>  [1] IPO_1.0.0           CAMERA_1.30.0       rsm_2.8            
#>  [4] faahKO_1.13.0       xcms_1.50.0         Biobase_2.34.0     
#>  [7] ProtGenerics_1.6.0  BiocGenerics_0.20.0 mzR_2.8.0          
#> [10] Rcpp_0.12.7        
#> 
#> loaded via a namespace (and not attached):
#>  [1] zoo_1.7-13             splines_3.3.1          lattice_0.20-34       
#>  [4] colorspace_1.2-7       snow_0.4-2             htmltools_0.3.5       
#>  [7] stats4_3.3.1           yaml_2.1.13            chron_2.3-47          
#> [10] survival_2.39-5        RBGL_1.50.0            foreign_0.8-67        
#> [13] BiocParallel_1.8.0     RColorBrewer_1.1-2     multcomp_1.4-6        
#> [16] plyr_1.8.4             stringr_1.1.0          lsmeans_2.23-5        
#> [19] munsell_0.4.3          gtable_0.2.0           mvtnorm_1.0-5         
#> [22] codetools_0.2-15       coda_0.18-1            evaluate_0.10         
#> [25] latticeExtra_0.6-28    knitr_1.14             MassSpecWavelet_1.40.0
#> [28] TH.data_1.0-7          acepack_1.3-3.3        xtable_1.8-2          
#> [31] scales_0.4.0           formatR_1.4            S4Vectors_0.12.0      
#> [34] Hmisc_3.17-4           graph_1.52.0           gridExtra_2.2.1       
#> [37] RANN_2.5               ggplot2_2.1.0          digest_0.6.10         
#> [40] stringi_1.1.2          grid_3.3.1             tools_3.3.1           
#> [43] sandwich_2.3-4         magrittr_1.5           tibble_1.2            
#> [46] Formula_1.2-1          cluster_2.0.5          MASS_7.3-45           
#> [49] Matrix_1.2-7.1         data.table_1.9.6       estimability_1.1-1    
#> [52] assertthat_0.1         rmarkdown_1.1          rpart_4.1-10          
#> [55] igraph_1.0.1           multtest_2.30.0        nnet_7.3-12           
#> [58] nlme_3.1-128