smoothOutlierBins: Smooth outlier bins after normalization

Description Usage Arguments Value Author(s) Examples

Description

Smooth outlier bins after normalization.

Usage

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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..

Author(s)

Ilari Scheinin

Examples

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

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