byChromArm {biscuiteer} | R Documentation

## 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)

[Package biscuiteer version 1.0.0 Index]