Analysis of Metabolomics GC/MS Data

---

Documentation for package ‘flagme’ version 1.54.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

Help Pages

addAMDISPeaks	Add AMDIS peak detection results
addChromaTOFPeaks	Add ChromaTOF peak detection results
addXCMSPeaks	addXCMSPeaks
betweenAlignment	Data Structure for "between" alignment of many GCMS samples
betweenAlignment-class	Data Structure for "between" alignment of many GCMS samples
betweenAlignment-method	Data Structure for "between" alignment of many GCMS samples
betweenAlignment-show	Data Structure for "between" alignment of many GCMS samples
calcTimeDiffs	Calculate retention time shifts from profile alignments
clusterAlignment	Data Structure for a collection of all pairwise alignments of GCMS runs
clusterAlignment-class	Data Structure for a collection of all pairwise alignments of GCMS runs
clusterAlignment-plot	Data Structure for a collection of all pairwise alignments of GCMS runs
clusterAlignment-show	Data Structure for a collection of all pairwise alignments of GCMS runs
corPrt	Retention Time Penalized Correlation
de_Duper	deDuper
distToLib	distToLib
dp	Dynamic programming algorithm, given a similarity matrix
dynRT	dynRT
eitherMatrix-class	A class description
exportSpectra	exportSpectra
gatherInfo	Gathers abundance informations from an alignment
headToTailPlot	Head to tail plot
importSpec	importSpec
imputePeaks	Imputatin of locations of peaks that were undetected
matchSpec	matchSpec
multipleAlignment	Data Structure for multiple alignment of many GCMS samples
multipleAlignment-class	Data Structure for multiple alignment of many GCMS samples
multipleAlignment-class,	Data Structure for multiple alignment of many GCMS samples
multipleAlignment-method	Data Structure for multiple alignment of many GCMS samples
multipleAlignment-show,	Data Structure for multiple alignment of many GCMS samples
ndpRT	Retention Time Penalized Normalized Dot Product
normDotProduct	Normalized Dot Product
parseChromaTOF	Parser for ChromaTOF files
parseELU	Parser for ELU files
peaksAlignment	Data Structure for pairwise alignment of 2 GCMS samples
peaksAlignment-class	Data Structure for pairwise alignment of 2 GCMS samples
peaksAlignment-plot	Data Structure for pairwise alignment of 2 GCMS samples
peaksAlignment-show	Data Structure for pairwise alignment of 2 GCMS samples
peaksDataset	Data Structure for raw GCMS data and peak detection results
peaksDataset-class	Data Structure for raw GCMS data and peak detection results
peaksDataset-plot	Data Structure for raw GCMS data and peak detection results
peaksDataset-show	Data Structure for raw GCMS data and peak detection results
plot-method	Data Structure for a collection of all pairwise alignments of GCMS runs
plot-method	Data Structure for pairwise alignment of 2 GCMS samples
plot-method	Data Structure for raw GCMS data and peak detection results
plotAlignedFrags	plotAlignedFrags
plotAlignment-method	plotAlignment
plotChrom-method	Plotting functions for GCMS data objects
plotClustAlignment-method	plotClustAlignment
plotFrags	plotFrags
plotImage	Plot of images of GCMS data
plotImage-method	Plot of images of GCMS data
progressiveAlignment	Data Structure for progressive alignment of many GCMS samples
progressiveAlignment-class	Data Structure for progressive alignment of many GCMS samples
progressiveAlignment-show	Data Structure for progressive alignment of many GCMS samples
retFatMatrix	retFatMatrix
rmaFitUnit	Fits a robust linear model (RLM) for one metabolite
show,	Data Structure for "between" alignment of many GCMS samples
show-method	Data Structure for a collection of all pairwise alignments of GCMS runs
show-method	Data Structure for pairwise alignment of 2 GCMS samples
show-method	Data Structure for raw GCMS data and peak detection results
show-method	Data Structure for progressive alignment of many GCMS samples
show-method	Store the raw data and optionally, information regarding signal peaks for a number of GCMS runs