binCoverage: Bin CpG or CpH coverage to simplify and improve CNA...

In trichelab/biscuiteer: Convenience Functions for Biscuit

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)

trichelab/biscuiteer documentation built on March 4, 2024, 12:22 a.m.