CMSraw-class: A class to hold chromatography-mass spectrometry raw data and...

Description Slots Utility functions Accessors Examples

Description

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.

Slots

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.

Utility functions

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.

Accessors

We have the following accessor functions:

colData:

Gets the DataFrame containing phenotype and sample information.

Examples

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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)
}

yamss documentation built on Nov. 8, 2020, 6:57 p.m.