correctBins: Correct binned read counts for GC content and mappability

In QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

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 specifying 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.

Author(s)

Ilari Scheinin

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)

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.

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