QDNAseq (version 1.8.0)

compareToReference: Divide binned read counts with those of reference samples

Description

Divide binned read counts with those of reference samples.

Usage

compareToReference(object, references, force=FALSE)

Arguments

object

An object of class QDNAseqCopyNumbers.

references

A numeric vector of indexes of the reference sample. Must be the same length as there are samples in object. When NA, the sample will be kept as is. When FALSE, the sample will be removed from the output. As an example, object contains three samples: tumor1, tumor2, and normal2. There is no reference for tumor1, but normal2 is a matched normal sample from the same patient as tumor2. The keep tumor1 as is, but to divide tumor2 with normal2, argument references should be c(NA, 3, FALSE).

force

Whether to force the operation even when downstream data will be lost.

Value

Returns a QDNAseqCopyNumbers object with the desired samples divided by the signal of their reference samples.

Examples

data(LGG150)
readCounts <- LGG150
readCountsFiltered <- applyFilters(readCounts)
readCountsFiltered <- estimateCorrection(readCountsFiltered)
copyNumbers <- correctBins(readCountsFiltered)
copyNumbersNormalized <- normalizeBins(copyNumbers)
copyNumbersSmooth <- smoothOutlierBins(copyNumbersNormalized)
# Note: the following command will compare the sample to itself, which
# does not really make sense:
tumorVsNormal <- compareToReference(copyNumbersSmooth, c(1))