normalizeGC: Normalization of read count data by GC content

In CNOGpro: Copy Numbers of Genes in prokaryotes

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)

Example output

Loading required package: seqinr
Normalizing read counts for GC bias...
Overall values for chromosome  CP003467 :
Median read count:  66 
Median GC percentage:  0.17 
Calculating per-read weight based on GC percentage...
Successfully normalized chromosome  CP003467 

CNOGpro documentation built on May 2, 2019, 5:57 a.m.