calcGC2 {genoset} | R Documentation

## Calculate GC Percentage in sliding window

### Description

Local GC content can be used to remove GC artifacts from copynumber data (see Diskin et al, Nucleic Acids Research, 2008, PMID: 18784189). This function will calculate GC content fraction in expanded windows around a set of ranges following example in http://www.bioconductor.org/help/course-materials/2012/useR2012/Bioconductor-tutorial.pdf. Values are as.integer( 1e4 * fraction ) for space reasons.

### Usage

    calcGC2(dna)

### Arguments

`dna` | BSgenome or DNAStringSet

### Value

SimpleRleList, integer 1e4 * GC fraction, chromosomes 1:22, X and Y

### Examples

    ## Not run:  library(BSgenome.Hsapiens.UCSC.hg19)
    ## Not run:  gc = calcGC2(Hsapiens)

[Package genoset version 1.45.1 Index]