applyThresholds {seqCNA} | R Documentation

## 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.

### Author(s)

David Mosen-Ansorena

### 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)

[Package seqCNA version 1.40.0 Index]