normalizeBins: Normalizes binned read counts

In ccagc/QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

Normalizes binned read counts

Description

Normalizes binned read counts.

Usage

normalizeBins(object, method="median", force=FALSE, verbose=getOption("QDNAseq::verbose",
  TRUE))

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.
verbose	If TRUE, verbose messages are produced.

Value

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

Author(s)

Ilari Scheinin

Examples

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

ccagc/QDNAseq documentation built on July 28, 2024, 3:46 p.m.