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

Value

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) 

Results