CMSraw-class {yamss} | R Documentation |
This class saves the data from raw mass spectral data files in a
data.table
and is used in subsequent processing. Objects of
this class are created by the readMSdata
function.
colData
:a DataFrame
of phenotype and sample information.
rawDT
:a data.table
of raw spectral information.
mzParams
:a list containing the minimum and maximum M/Z value and number of scans in each sample.
We have the following utility functions:
show
:The show method; prints the object.
getEICS
:Gets extracted ion chromatograms (EICs) for the supplied M/Z ranges.
We have the following accessor functions:
colData
:Gets the DataFrame
containing phenotype and sample information.
data(cmsRawExample) cmsRawExample if (require(mtbls2)) { data(mtbls2) filepath <- file.path(find.package("mtbls2"), "mzData") files <- list.files(filepath, pattern = "MSpos-Ex1", recursive = TRUE, full.names = TRUE)[1] colData <- DataFrame(group = "wild-type") cmsRaw <- readMSdata(files = files, colData = colData, verbose = TRUE) colData(cmsRaw) }