xcms (version 1.48.0)

xcmsSet: 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, lockMassFreq=FALSE,
		mslevel=NULL, nSlaves=0, progressCallback=NULL, scanrange = NULL, ...)

Arguments

files

path names of the NetCDF/mzXML files to read

snames

sample names. By default the file name without extension is used.

sclass

sample classes.

phenoData

data.frame or AnnotatedDataFrame defining the sample names and classes and other sample related properties. If not provided, the argument sclass or the subdirectories in which the samples are stored will be used to specify sample grouping.

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. If none of the two packages is available it uses the parallel package for parallel processing on multiple CPUs of the current machine.

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

Value

A xcmsSet object.

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.

If phenoData is provided, it is stored to the phenoData slot of the returned xcmsSet class. If that data.frame contains a column named “class”, its content will be returned by the sampclass method and thus be used for the group/class assignment of the individual files (e.g. for peak grouping etc.). For more details see the help of the xcmsSet-class.

The step size (in m/z) to use for profile generation can be submitted either using the profparam argument (e.g. profparam=list(step=0.1)) or by submitting step=0.1.

The feature/peak detection algorithm can be specified with the method argument which defaults to the "matchFilter" method (findPeaks.matchedFilter). Possible values are returned by getOption("BioC")$xcms$findPeaks.methods.

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.

See Also

xcmsSet-class, findPeaks, profStep, profMethod, xcmsPapply