QDNAseq (version 1.8.0)

correctBins: Correct binned read counts for GC content and mappability

Description

Correct binned read counts for GC content and mappability.

Usage

correctBins(object, fit=NULL, method="ratio", adjustIncompletes=TRUE, ...)

Arguments

object

An QDNAseqReadCounts object with counts data.

fit

An optional matrix of values to use for the correction. If NULL (default), assay data fit from object is used. If it is missing, it is generated with a call to estimateCorrection().

method

A character(1) string speficying the correction method. ratio (default) divides counts with fit. median calculates the median fit, and defines the correction for bins with GC content gc and mappability map as median(fit) - fit(gc,map), which is added to counts. Method none leaves counts untouched.

adjustIncompletes

A boolean(1) specifying whether counts for bins with uncharacterized nucleotides (N's) in their reference genome sequence should be adjusted by dividing them with the percentage of characterized (A, C, G, T) nucleotides. Defaults to TRUE.

...

Additional arguments passed to estimateCorrection().

Value

Returns a QDNAseqCopyNumbers object with assay data element copynumber.

See Also

Internally, loess is used to fit the regression model.

Examples

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