segmentMD {MDTS} | R Documentation |
This function will return a GRanges object containing the copy number segments of all families in the input minimum distance matrix. It calls segment() from DNAcopy (alpha=0.001, undo.splits="sdundo", undo.SD=4).
segmentMD(md, bins, alpha = 0.001, undo.splits = "sdundo", undo.SD = 4, mc.cores = 1)
md |
The minimum distance matrix produced by calcMD. |
bins |
The set of bins determined by calcBins. |
alpha |
Controls the alpha option in calling DNAcopy::segment() |
undo.splits |
Controls the undo.splits option in DNAcopy::segment() |
undo.SD |
Controls the undo.SD option in calling DNAcopy::segment() |
mc.cores |
The number of cores to use for multi-threaded analysis. Defaults to 1. |
A data.frame
containing the segmented regions based to be
parsed by denovoDeletions()
minimum distance.
load(system.file("extdata", 'bins.RData', package = "MDTS")) load(system.file("extdata", 'counts.RData', package = "MDTS")) load(system.file("extdata", 'pD.RData', package = "MDTS")) mCounts <- normalizeCounts(counts, bins) md <- calcMD(mCounts, pD) cbs <- segmentMD(md, bins)