XCMS.align.centWave: XCMS.align.centWave

In yufree/xMSanalyzer: xMSanalyzer: R package for data analysis, comparison, and annotation of metabolomics data.

Description

Wrapper function for XCMS using the centwave alignment algorithm.

Usage

XCMS.align.centWave(cdfloc, XCMS.outloc, ppm.list = c(10), mz.diff.list = c(-0.001), 
    sn.thresh.list = c(10), prefilter.list = c(3, 100), bw.val = c(10), 
    groupval.method = "medret", step.list = c(0.1), max = 50, minfrac.val = 0.5, 
    minsamp.val = 1, mzwid.val = 0.25, sleep.val = 0, run.order.file = NA, 
    subs = NA, retcor.method = "obiwarp", retcor.family = "symmetric", 
    retcor.plottype = "deviation", peakwidth = c(20, 50), nSlaves = 2)

Arguments

cdfloc	The folder where all CDF/mzXML files to be processed are located. For example "C:/CDF/"
XCMS.outloc	The folder where alignment output will be written. For example "C:/CDFoutput/"
ppm.list	list containing values for maximal tolerated m/z deviation in consecutive scans, in ppm
mz.diff.list	list containing values for the minimum difference for features with retention time overlap. eg: c(0.001,0.1)
sn.thresh.list	list containing values for signal to noise ratio cutoff variable. eg: c(3,10)
prefilter.list	prefiltering values c(k,l) where mass traces that do not contain at least k peaks with intensity>=l are filtered
bw.val	bandwidth value
groupval.method	Conflict resolution method while calculating peak values for each group. eg: "medret" or "maxint"
step.list	list containing values for the step size. eg: c(0.1,1)
max	Value for maxnimum number of peaks per EIC variable. eg: 50
minfrac.val	minimum fraction of samples necessary in at least one of the sample groups for it to be a valid group
minsamp.val	minimum number of samples necessary in at least one of the sample groups for it to be a valid group
mzwid.val	width of overlapping m/z slices to use for creating peak density chromatograms and grouping peaks across samples
sleep.val	seconds to pause between plotting successive steps of the peak grouping algorithm. peaks are plotted as points showing relative intensity. identified groups are flanked by dotted vertical lines.
run.order.file	Name of a tab-delimited file that includes sample names sorted by the order in which they were run(sample names must match the CDF file names)
subs	If not all the CDF files in the folder are to be processed, the user can define a subset using this parameter. For example, subs=15:30, or subs=c(2,4,6,8)
retcor.method	Method for aligning retention times across samples. eg: "loess" or "obiwarp"
retcor.family	Used by matchedFilter alignment method. Use "gaussian" to perform fitting by least squares without outlier removal. Or "symmetric" to use a redescending M estimator with Tukey's biweight function that allows outlier removal.
retcor.plottype	Used by both matchedFilter and centWave alignment methods. eg: "deviation" or "mdevden"
peakwidth	Chromtagrophic peak width in seconds. eg: c(20,50)
nSlaves	Number of computing cores to be used. eg: 2

Details

This is a wrapper function based on the xcms Bioconductor package for preprocessing/analysis of mass spectral data. The resulting tables containing m/z, retention time, and mean peak intensities in each sample are stored at each parameter combination.

Value

A matrix, with columns of m/z values, elution times, mean signal strengths in each spectrum

Note

Please refer to the xcms manual in Bioconductor for more details.

Author(s)

Karan Uppal

References

Tautenhahn R, Bottcher C, Neumann S. Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics. 2008 Nov 28.

yufree/xMSanalyzer documentation built on May 4, 2019, 6:35 p.m.