loadXcmsData: LC-MS preprocessing result test data sets

In sneumann/xcms: LC-MS and GC-MS Data Analysis

LC-MS preprocessing result test data sets

Description

Data sets with 'xcms' preprocessing results are provided within the 'xcms' package and can be loaded with the 'loadXcmsData' function. The available Test data sets are:

- 'xdata': an [XCMSnExp()] object with the results from a 'xcms'-based pre-processing of an LC-MS untargeted metabolomics data set. The raw data files are provided in the 'faahKO' R package.

- 'xmse': an [XcmsExperiment()] object with the results from an 'xcms'-based pre-processing of an LC-MS untargeted metabolomics data set (same original data set and pre-processing settings as for the 'xdata' data set). The pre-processing of this data set is described in detail in the *xcms* vignette of the 'xcms' package.

- 'faahko_sub': an [XCMSnExp()] object with identified chromatographic peaks in 3 samples from the data files in the 'faahKO' R package.

- 'faahko_sub2': an [XcmsExperiment()] object with identified chromatographic peaks in 3 samples from the data files in the 'faahKO' R package.

Data sets can also be loaded using 'data', which would however require to update objects to point to the location of the raw data files. The 'loadXcmsData' loads the data and ensures that all paths are updated accordingly.

Usage

loadXcmsData(x = c("xmse", "xdata", "faahko_sub", "faahko_sub2"))

Arguments

x	For 'loadXcmsData': 'character(1)' with the name of the data file (object) to load.

Examples

library(xcms)
xdata <- loadXcmsData()

sneumann/xcms documentation built on April 26, 2024, 3:05 a.m.