xcmsSet: Constructor for xcmsSet objects which finds peaks in...

Description Usage Arguments Details Value Author(s) See Also

View source: R/xcmsSet.R

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

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xcmsSet(files = NULL, snames = NULL, sclass = NULL, phenoData = NULL,
        profmethod = "bin", profparam = list(),
        polarity = NULL, lockMassFreq=FALSE,
		mslevel=NULL, nSlaves=0, progressCallback=NULL,
                scanrange = NULL, ...)

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

lockMassFreq

Performs correction for Waters LockMass function

mslevel

perform peak picking on data of given mslevel

nSlaves

number of slaves/cores to be used for parallel peak detection. MPI is used if installed, otherwise the snow package is employed for multicore support.

progressCallback

function to be called, when progressInfo changes (useful for GUIs)

scanrange

scan range to read

...

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 explicitly. The default (NULL) is to read all scans.

The lock mass correction allows for the lock mass scan to be added back in with the last working scan. This correction gives better reproducibility between sample sets.

Value

A xcmsSet object.

Author(s)

Colin A. Smith, csmith@scripps.edu

See Also

xcmsSet-class, findPeaks, profStep, profMethod, xcmsPapply


sneumann/xcms-presvnbridge documentation built on May 30, 2019, 6:02 a.m.