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

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)