byChromArm {biscuiteer} | R Documentation |
This function splits an object by chromosome arm, which tends to make parallelization much easier, as cross-arm dependencies are unusual. Therefore, the larger chromosomes can be split across processes or machines without worrying much about data starvation for processes on smaller chromosomes.
byChromArm(x, arms = NULL)
x |
Any object with a GRanges in it: bsseq, SummarizedExperiment... |
arms |
Another GRanges, but specifying chromosome arms (DEFAULT: NULL) |
A list, List, or *list, with pieces of x by chromosome arm
orig_bed <- system.file("extdata", "MCF7_Cunha_chr11p15.bed.gz", package="biscuiteer") orig_vcf <- system.file("extdata", "MCF7_Cunha_header_only.vcf.gz", package="biscuiteer") bisc <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf, merged = FALSE) reg <- GRanges(seqnames = rep("chr11",5), strand = rep("*",5), ranges = IRanges(start = c(0,2.8e6,1.17e7,1.38e7,1.69e7), end= c(2.8e6,1.17e7,1.38e7,1.69e7,2.2e7)) ) names(reg) <- as.character(reg) arms <- byChromArm(bisc, arms = reg)