calcGC {genoset} | R Documentation

## Calculate GC Percentage in windows

### 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. Currently all ranges are tabulated, later I may do letterFrequencyInSlidingWindow for big windows and then match to the nearest.

### Usage

    calcGC(object, bsgenome, expand = 1e+06, bases = c("G", "C"))

### Arguments

`object` | GenomicRanges or GenoSet
`bsgenome` | BSgenome, like Hsapiens from BSgenome.Hsapiens.UCSC.hg19 or DNAStringSet.
`expand` | scalar integer, amount to expand each range before calculating gc
`bases` | character, alphabet to count, usually c('G', 'C'), but 'N' is useful too

### Value

named numeric vector, fraction of nucleotides that are G or C in expanded ranges of `object`

### Examples

    ## Not run:  library(BSgenome.Hsapiens.UCSC.hg19)
    ## Not run:  gc = calcGC(genoset.ds, Hsapiens)

[Package genoset version 1.45.1 Index]