
callBins(object, organism=c("human", "other"), method=c("CGHcall", "cutoff"), cutoffs=log2(c(deletion = 0.5, loss = 1.5, gain = 2.5, amplification = 10)/2), ...)
CGHcall
for more details. This is only used for
chromosome arm information when “prior” is set to “all”
or “auto” (and samplesize > 20). Ignored when method
is
not “CGHcall”.CGHcall
.QDNAseqCopyNumbers
with calling
results added.
When using method “cutoff”, the default values assume a uniform cell population and correspond to thresholds of (assuming a diploid genome) 0.5, 1.5, 2.5, and 10 copies to distinguish between homozygous deletions, (hemizygous) losses, normal copy number, gains, and amplifications, respectively. When using with cancer samples, these values might require adjustments to account for tumor cell percentage.
CGHcall
and ExpandCGHcall
of
the CGHcall package are used when method=“CGHcall”.
data(LGG150)
readCounts <- LGG150
readCountsFiltered <- applyFilters(readCounts)
readCountsFiltered <- estimateCorrection(readCountsFiltered)
copyNumbers <- correctBins(readCountsFiltered)
copyNumbersNormalized <- normalizeBins(copyNumbers)
copyNumbersSmooth <- smoothOutlierBins(copyNumbersNormalized)
copyNumbersSegmented <- segmentBins(copyNumbersSmooth)
copyNumbersSegmented <- normalizeSegmentedBins(copyNumbersSegmented)
copyNumbersCalled <- callBins(copyNumbersSegmented)
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