atRegions {biscuiteer} | R Documentation

## 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)

[Package biscuiteer version 1.4.0 Index]