QDNAseq (version 1.8.0)

smoothOutlierBins: Smooth outlier bins after normalization

Description

Smooth outlier bins after normalization.

Usage

smoothOutlierBins(object, logTransform=TRUE, force=FALSE, ...)

Arguments

object

A QDNAseqCopyNumbers object with copynumber data.

logTransform

If TRUE (default), data will be log2-transformed.

force

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

...

Additional arguments passed to smooth.CNA.

Value

Returns a QDNAseqCopyNumbers object with the values for outliers smoothed. See smooth.CNA for more details. If logTransform is TRUE, these signals are log2-transformed prior to smoothing, but afterwards back-transformed..

Examples

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