Description Usage Arguments Details Value Note Author(s)
Runs XCMS using the matchedFilter alignment algorithm at different parameter settings.
1 2 3 4 5 | XCMS.align.matchedFilter(cdfloc, XCMS.outloc, step.list = c(0.001),
mz.diff.list = c(0.1), sn.thresh.list = c(3), max = 50, bw.val = c(10),
minfrac.val = 0.5, minsamp.val = 2, mzwid.val = 0.25, sleep.val = 0,
run.order.file = NA, subs = NA, retcor.family = "symmetric",
retcor.plottype = "mdevden", groupval.method = "medret")
|
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/" |
step.list |
list containing values for the step size |
mz.diff.list |
list containing values for the minimum difference for features with retention time overlap |
sn.thresh.list |
list containing values for signal to noise ratio cutoff variable |
max |
Value for maxnimum number of peaks per EIC variable: eg: 5 |
bw.val |
bandwidth value |
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.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" |
groupval.method |
Conflict resolution method while calculating peak values for each group. eg: "medret" or "maxint" |
This is a wrapper function based on the xcms Bioconductor package for preprocessing/analysis of mass spectral data. The XCMS.align utility performs serial sample processing at multiple combinations of four parameters: step (the step size; default values: 0.001, 0.01, 0.1), mzdiff (minimum difference for features with retention time overlap; default values: 0.001, 0.01, 0.1), snthresh (signal-to-noise ratio cutoff; default values: 3, 6, 10), and max (maximum number of peaks per EIC; default values: 5, 10). 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 <kuppal2@emory.edu>
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