biscuiteer-methods {biscuiteer} | R Documentation

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

### 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

[Package biscuiteer version 1.1.0 Index]