CMSraw-class: A class to hold chromatography-mass spectrometry raw data and...
In hansenlab/yamss: Tools for high-throughput metabolomics

Description Slots Utility functions Accessors Examples

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"), "mzML")
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)
}