Skip to contents

LC-MS preprocessing result test data sets

Source: R/loadXcmsData.R
loadXcmsData.Rd

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()