R: Normalization of read count data by GC content

normalizeGC {CNOGpro} | R Documentation

## Normalization of read count data by GC content

### Description

Manipulates count values from windows of comparatively high or low GC content so as to bring the counts more in line with those from median GC-content windows.

### Usage

    normalizeGC(experiment)

### Arguments

`experiment` | `experiment` An object of class `CNOGpro`.

### Details

Implements the Yoon et al. (2009) normalization scheme.

### Value

An object of class `CNOGpro`, containing a numeric vector `CorrReadsprWindow`.

### Author(s)

Ola Brynildsrud

### References

Yoon,S. et al. (2009) Sensitive and accurate detection of copy number variants using read depth of coverage. Genome Research, 19, 1586–1592.

### Examples

    data(carsonella)
    carsonella_normalized <- normalizeGC(carsonella)
    plotCNOGpro(carsonella_normalized)

[Package CNOGpro version 1.1 Index]