smoothOutlierBins {QDNAseq} | R Documentation

## 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)

[Package QDNAseq version 1.16.0 Index]