get_context_freq {SigsPack} | R Documentation |
Extracts the frequencies of the tri-nucleotide contexts in a given region of the genome. These frequencies are needed to normalize a mutational catalogue. The output can be input to normalize().
get_context_freq(genome, region = NULL)
genome |
a BSgenome object |
region |
a GRanges object, path, URL, connection or BEDFile object. |
matrix containing the frequencies of the trinucleotide contexts
gr<-GenomicRanges::GRanges(seqnames=c("chr1"), ranges=IRanges::IRanges(start=c(100000),end=c(1000000)), strand=c("+")) get_context_freq(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19, gr) get_context_freq(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19) ## Not run: get_context_freq(BSgenome.Hsapiens.UCSC.hg19::BSgenome.Hsapiens.UCSC.hg19, 'example.bed') ## End(Not run)