normalizeBins {QDNAseq} | R Documentation

## Normalizes binned read counts

### Description

Normalizes binned read counts.

### Usage

    normalizeBins(object, method="median", force=FALSE, verbose=getOption("QDNAseq::verbose",
      TRUE))

### Arguments

`object` | A `QDNAseqCopyNumbers` object with `copynumber` data.
`method` | A `character` string specifying the normalization method. Choices are "mean", "median" (default), or "mode". A partial string sufficient to uniquely identify the choice is permitted.
`force` | Running this function will remove possible segmentation and calling results. When they are present, running requires specifying `force` is `TRUE`.
`verbose` | If `TRUE`, verbose messages are produced.

### Value

Returns a `QDNAseqCopyNumbers` object with the assay data element `copynumber` scaled with the chosen method.

### Author(s)

Ilari Scheinin

### Examples

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

[Package QDNAseq version 1.24.0 Index]