compareToReference {QDNAseq} | R Documentation |
Divide binned read counts with those of reference samples.
compareToReference(object, references, force=FALSE)
object |
An object of class |
references |
A numeric vector of indexes of the reference sample.
Must be the same length as there are samples in object. When |
force |
Whether to force the operation even when downstream data will be lost. |
Returns a QDNAseqCopyNumbers
object with the desired samples
divided by the signal of their reference samples.
Ilari Scheinin
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))