seqCNA (version 1.18.0)

applyThresholds: Apply thresholds on the segmented profile in order to call copy numbers.

Description

Given a set of thresholds and the copy number of the lower resulting range, copy numbers are called.

Usage

applyThresholds(rco, thresholds, min.CN)

Arguments

rco

A SeqCNAInfo-class object, with read count (RC) and genomic information, normally the output of the runGLAD function.

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.

Value

A SeqCNAInfo-class object, with additional information on the copy numbers called for each genomic window.

Examples

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)