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)