xcmsSet {xcms}R Documentation

Constructor for xcmsSet objects which finds peaks in NetCDF/mzXML files

Description

This function handles the construction of xcmsSet objects. It finds peaks in batch mode and pre-sorts files from subdirectories into different classes suitable for grouping.

Usage

xcmsSet(files = NULL, snames = NULL, sclass = NULL, phenoData = NULL,
        profmethod = "bin", profparam = list(),
        polarity = NULL, nSlaves=0, ...)

Arguments

files path names of the NetCDF/mzXML files to read
snames sample names
sclass sample classes
phenoData sample names and classes
profmethod method to use for profile generation
profparam parameters to use for profile generation
polarity filter raw data for positive/negative scans
nSlaves number of MPI-slaves to use for parallel peak detection, works only if Rmpi is installed properly, see xcmsPapply.
... further arguments to the findPeaks method of the xcmsRaw class

Details

The default values of the files, snames, sclass, and phenoData arguments cause the function to recursively search for readable files. The filename without extention is used for the sample name. The subdirectory path is used for the sample class. If the files contain both positive and negative spectra, the polarity can be selected explicitely. The default (NULL) is to read all scans.

Value

A xcmsSet object.

Author(s)

Colin A. Smith, csmith@scripps.edu

See Also

xcmsSet-class, findPeaks, profStep, profMethod


[Package xcms version 1.16.3 Index]