applyThresholds {seqCNA} | R Documentation |
Given a set of thresholds and the copy number of the lower resulting range, copy numbers are called.
applyThresholds(rco, thresholds, min.CN)
rco |
A |
thresholds |
A vector with values that establish the ranges for each copy number. |
min.CN |
The copy number of the lowest range defined by the thresholds. |
A SeqCNAInfo-class
object, with additional information on the copy numbers called for each genomic window.
David Mosen-Ansorena
data(seqsumm_HCC1143) rco = readSeqsumm(tumour.data=seqsumm_HCC1143) rco = applyFilters(rco, 0, 1, 0, 2, FALSE, plots=FALSE) rco = runSeqnorm(rco, plots=FALSE) rco = runGLAD(rco) ### CALLING ### thresholds = seq(-0.9,4,by=0.9) min.CN = 1 rco = applyThresholds(rco, thresholds, min.CN)