normalizeBins: Normalizes binned read counts

In QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

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)

Example output

38,819	total bins
38,819	of which in selected chromosomes
36,722	of which with reference sequence
33,347	final bins
Calculating correction for GC content and mappability
    Calculating fit for sample LGG150 (1 of 1) ...
Done.
Applying median normalization ...

QDNAseq documentation built on Nov. 8, 2020, 6:57 p.m.