byChromArm: A simple parallization step

In trichelab/biscuitEater: Convenience Functions for Biscuit

A simple parallization step

Description

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.

Usage

byChromArm(x, arms = NULL)

Arguments

x	Any object with a GRanges in it: bsseq, SummarizedExperiment...
arms	Another GRanges, but specifying chromosome arms (DEFAULT: NULL)

Value

 A list, List, or *list, with pieces of x by chromosome arm

Examples

  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)

trichelab/biscuitEater documentation built on March 2, 2024, 6:57 p.m.