biscuiteer-methods: bsseq class methods (VCF-centric) added by biscuiteer

In biscuiteer: Convenience Functions for Biscuit

Description

See biscuiteer manpage for package description

Usage

## S4 method for signature 'BSseq'
samples(object)

## S4 method for signature 'BSseq'
header(x)

## S4 method for signature 'BSseq'
meta(x)

## S4 method for signature 'BSseq'
fixed(x)

## S4 method for signature 'BSseq'
info(x)

## S4 method for signature 'BSseq,ANY'
geno(x)

Arguments

object	A bsseq object, preferably with !is.null(metadata(x)$vcfHeader)
x	A bsseq object, preferably with !is.null(metadata(x)$vcfHeader)

Details

biscuiteer adds VariantAnnotation methods to BSseq objects with VCF headers: samples,header,meta,fixed,info,geno

Due to inherited method signatures, the argument (singular) to the method may be named x or it may be named object. Either way, it is a BSseq object.

These add to the existing methods defined in package bsseq for class BSseq: [,length,sampleNames,sampleNames<-,pData,pData<-,show,combine

Those add to the methods BSseq inherits from SummarizedExperiment, such as: colData,rowRanges,metadata,subset,subsetByOverlaps,isDisjoint,&c.

Most of the biscuiteer methods operate on the VCF header, which readBiscuit likes to stuff into the metadata slot of BSseq objects it produces. Some may be handy for populating a BSseq object with QC stats, or querying those.

Value

  Depends on the method - usually a List-like object of some sort

See Also

RangedSummarizedExperiment

VCFHeader-class

BSseq-class

BSseq

biscuiteer documentation built on Nov. 8, 2020, 8:28 p.m.