filterLoci: Filter loci with zero coverage

In trichelab/biscuiteer: Convenience Functions for Biscuit

Filter loci with zero coverage

Description

Function potentially used to be a part of dmrseq. Included here to avoid dmrseq failing due to any number of reasons related to lack of coverage.

Usage

filterLoci(bsseq, testCovariate)

Arguments

bsseq	A bsseq object for filtering
testCovariate	The name of the pData column dmrseq will test on

Details

The code is adapted from the precheck loop of dmrseq::dmrseq

Value

          A bsseq object ready for dmrseq to use

See Also

dmrseq

WGBSeq

RRBSeq

Examples

  shuf_bed <- system.file("extdata", "MCF7_Cunha_chr11p15_shuffled.bed.gz",
                          package="biscuiteer")
  orig_bed <- system.file("extdata", "MCF7_Cunha_chr11p15.bed.gz",
                          package="biscuiteer")
  shuf_vcf <- system.file("extdata",
                          "MCF7_Cunha_shuffled_header_only.vcf.gz",
                          package="biscuiteer")
  orig_vcf <- system.file("extdata",
                          "MCF7_Cunha_header_only.vcf.gz",
                          package="biscuiteer")
  bisc1 <- readBiscuit(BEDfile = shuf_bed, VCFfile = shuf_vcf,
                       merged = FALSE)
  bisc2 <- readBiscuit(BEDfile = orig_bed, VCFfile = orig_vcf,
                       merged = FALSE)

  comb <- unionize(bisc1, bisc2)

  filt <- filterLoci(comb, "sampleNames")

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