calcGC2 {genoset} | R Documentation |
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.
calcGC2(dna)
dna |
BSgenome or DNAStringSet |
SimpleRleList, integer 1e4 * GC fraction, chromosomes 1:22, X and Y
## Not run: library(BSgenome.Hsapiens.UCSC.hg19) ## Not run: gc = calcGC2(Hsapiens)