genoset (version 1.28.2)

calcGC: 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

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

Examples

library(BSgenome.Hsapiens.UCSC.hg19)
gc = calcGC(genoset.ds, Hsapiens)