| denovoDeletions {MDTS} | R Documentation |
This function will return a single GRanges object containing all denovo deletions that passed filtering from a Circular Binary Segmentation object with supplementary information.
denovoDeletions(cbs, mCounts, bins)
cbs |
The output from segmentMD(). |
mCounts |
The normalized counts matrix output by normalizeCounts(). |
bins |
The set of bins determined by calcBins(). |
A GRanges object that reports all detected denovo deletions
passing requite filters.
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)
denovo = denovoDeletions(cbs, mCounts, bins)