Description Usage Arguments Details Value Note Author(s) References
Wrapper function for XCMS using the centwave alignment algorithm.
1 2 3 4 5 6 | 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)
|
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 |
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.
A matrix, with columns of m/z values, elution times, mean signal strengths in each spectrum
Please refer to the xcms manual in Bioconductor for more details.
Karan Uppal
Tautenhahn R, Bottcher C, Neumann S. Highly sensitive feature detection for high resolution LC/MS. BMC Bioinformatics. 2008 Nov 28.
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