Description Utility functions Accessors Examples
This class is based on the
SummarizedExperiment class. It holds
information on peak quantifications, M/Z and scan bounds, sample information,
and preprocessing metadata. Objects of the class can be constructed
We have the following utility functions:
The show method; prints the object.
We have the following accessor functions:
DataFrame containing phenotype and sample information.
Gets the value used to threshold the density for peak calling.
Gets the quantiles of the nonzero values in the density estimate.
DataFrame of M/Z bounds, scan bounds, and ID numbers
for detected peaks.
Gets the matrix of peak quantifications (rows: peaks, columns: samples).
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## Construct a fake class quants <- matrix(rnorm(12*5000), nrow = 5000, ncol = 12) bounds <- cbind(mzmin = seq(from = 100, to = 1100, length.out = 5000), mzmax = seq(from = 100, to = 1100, length.out = 5000) + 0.1, scan.min = rep(10,5000), scan.max = rep(20, 5000), peaknum = 1:5000) cmsobj <- CMSslice(assays = SimpleList(peakQuants = quants), rowData = DataFrame(bounds)) head(peakQuants(cmsobj)) ## A better example which takes 20s to run ## Not run: data(cmsRawExample) cmsProc <- bakedpi(cmsRawExample, dbandwidth = c(0.01, 10), dgridstep = c(0.01, 1), dortalign = TRUE, mzsubset = c(500,510)) cutoff <- densityQuantiles(cmsProc)["99.9 sliced <- slicepi(cmsProc, cutoff = cutoff, verbose = TRUE) sliced ## End(Not run)
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