biscuitMetadata: Biscuit metadata from VCF header

In trichelab/biscuitEater: Convenience Functions for Biscuit

Biscuit metadata from VCF header

Description

Returns metadata from a Biscuit run using either a supplied VCF file or the vcfHeader metadata element from the bsseq object

Usage

biscuitMetadata(bsseq = NULL, VCF = NULL)

getBiscuitMetadata(bsseq = NULL, VCF = NULL)

Arguments

bsseq	A bsseq object with a vcfHeader element (DEFAULT: NULL)
VCF	A tabix'ed VCF file (can just be the header information) from which the bsseq vcfHeader element is derived (DEFAULT: NULL)

Value

  Information regarding the Biscuit run

Functions

• getBiscuitMetadata(): Alias for biscuitMetadata

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)

  meta <- biscuitMetadata(bisc)
  

trichelab/biscuitEater documentation built on March 2, 2024, 6:57 p.m.