filterLoci {biscuiteer} | R Documentation

## 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")

[Package biscuiteer version 1.0.0 Index]