smoothOutlierBins: Smooth outlier bins after normalization

In ccagc/QDNAseq: Quantitative DNA Sequencing for Chromosomal Aberrations

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..

Author(s)

Ilari Scheinin

Examples

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

ccagc/QDNAseq documentation built on Feb. 2, 2023, 12:56 p.m.