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,
        profmethod = "bin", profparam = list(), ...)

Arguments

files path names of the NetCDF/mzXML files to read
snames sample names
sclass sample classes
profmethod method to use for profile generation
profparam parameters to use for profile generation
... further arguments to the findPeaks method of the xcmsRaw class

Details

The default values of the files, snames, and sclass 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.

Value

A xcmsSet object.

Note

Author(s)

Colin A. Smith, csmith@scripps.edu

See Also

xcmsSet-class, findPeaks, profStep, profMethod


[Package xcms version 1.4.0 Index]