QDNAseq (version 1.8.0)

normalizeBins: Normalizes binned read counts

Description

Normalizes binned read counts.

Usage

normalizeBins(object, method="median", force=FALSE)

Arguments

object

A QDNAseqCopyNumbers object with copynumber data.

method

A character string specifying the normalization method. Choices are "mean", "median" (default), or "mode". A partial string sufficient to uniquely identify the choice is permitted.

force

Running this function will remove possible segmentation and calling results. When they are present, running requires specifying force is TRUE.

Value

Returns a QDNAseqCopyNumbers object with the assay data element copynumber scaled with the chosen method.

Examples

data(LGG150)
readCounts <- LGG150
readCountsFiltered <- applyFilters(readCounts)
readCountsFiltered <- estimateCorrection(readCountsFiltered)
copyNumbers <- correctBins(readCountsFiltered)
copyNumbersNormalized <- normalizeBins(copyNumbers)