binCoverage {biscuiteer} | R Documentation

## Bin CpG or CpH coverage to simplify and improve CNA "sketching"

### Description

Example usage for E-M

### Usage

    binCoverage(
      bsseq,
      bins,
      which = NULL,
      QDNAseq = TRUE,
      readLen = 100,
      paired = TRUE
    )

### Arguments

`bsseq` | A bsseq object - supplied to getCoverage()
`bins` | Bins to summarize over - from tileGenome or QDNAseq.xxYY
`which` | Limit to specific regions? - functions as an import() (DEFAULT: NULL)
`QDNAseq` | Return a QDNAseqReadCounts? - if FALSE, returns a GRanges (DEFAULT: TRUE)
`readLen` | Correction factor for coverage - read length in bp (DEFAULT: 100)
`paired` | Whether the data are from paired-end sequencing (DEFAULT: TRUE)

### Details

NOTE: As of early Sept 2019, QDNAseq did not have hg38 capabilities. If you desire to use the hg38 genome, biscuiteer suggests you use a GRanges object to define your bins.

NOTE: As of late July 2020, biscuiteer has started implemented support for hg38, hg19, mm10, and mm9 for bisulfite-specific features, including adaptive GC-content computation and SV integration for adjusting CNV ends.

### Value

        Binned read counts

### Examples

      bins <- GRanges(seqnames = rep("chr11",10),
                      strand = rep("*",10),
                      ranges = IRanges(start=100000*0:9, width=100000)
                     )

      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))
                     )

      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)

      bc <- binCoverage(bsseq = bisc, bins = bins, which = reg, QDNAseq = FALSE)

[Package biscuiteer version 1.6.0 Index]