atRegions: Summarize a bsseq dataset over defined regions

In trichelab/biscuitEater: Convenience Functions for Biscuit

Summarize a bsseq dataset over defined regions

Description

Calls summarizeBsSeqOver to summarize a bsseq object over provided DNA regions. Useful for exploring genomic data using cBioPortal.

Usage

atRegions(bsseq, regions, mappings = NULL, nm = "POETICname", ...)

Arguments

bsseq	A bsseq object
regions	A GRanges or GRangesList of regions
mappings	A mapping table with rownames(mappings) == colnames(bsseq) (DEFAULT: NULL)
nm	Column of the mapping table to map to (DEFAULT: "POETICname")
...	Other arguments to pass to summarizeBsSeqOver

Value

     GRanges with summarized information about the bsseq object
             for the given DNA regions

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))
                )
  regions <- atRegions(bsseq = bisc, regions = reg)

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