ModBamResult-class: Modbam methylation results
In Shians/NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing

ModBamResult-class

R Documentation

Modbam methylation results

Description

A ModBamResult object stores modbam data used for NanoMethViz visualisation. It contains stores a ModBamFiles object, sample information and optional exon information. The object is constructed using the ModBamResult() constructor function described in "Usage".

Usage

## S4 method for signature 'ModBamResult'
methy(object)

## S4 replacement method for signature 'ModBamResult,ModBamFiles'
methy(object) <- value

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

## S4 replacement method for signature 'ModBamResult,data.frame'
samples(object) <- value

## S4 method for signature 'ModBamResult'
exons(object)

## S4 replacement method for signature 'ModBamResult,data.frame'
exons(object) <- value

## S4 method for signature 'ModBamResult'
mod_code(object)

## S4 replacement method for signature 'ModBamResult,character'
mod_code(object) <- value

ModBamResult(methy, samples, exons = NULL, mod_code = "m")

Arguments

`object`	the ModBamResult object.
`value`	the mod code.
`methy`	a ModBamFiles object.
`samples`	the data.frame of sample annotation containing at least columns sample and group.
`exons`	(optional) the data.frame of exon information containing at least columns gene_id, chr, strand, start, end, transcript_id and symbol.
`mod_code`	a character with the mod code of interest. Defaults to "m" for 5mC. See details for other options.

Details

The possible tags for mod_code can be found at https://samtools.github.io/hts-specs/SAMtags.pdf under the 'Base modifications' section.

Value

a NanoMethResult object to be used with plotting functions

a ModBamFiles data.frame.

the sample annotation.

the exon annotation.

the mod code.

Functions

methy(ModBamResult): modbam information getter.
methy(object = ModBamResult) <- value: modbam information setter.
samples(ModBamResult): sample annotation getter.
samples(object = ModBamResult) <- value: sample annotation setter.
exons(ModBamResult): exon annotation getter.
exons(object = ModBamResult) <- value: exon annotation setter.
mod_code(ModBamResult): mod code getter.
mod_code(object = ModBamResult) <- value: mod code setter.
ModBamResult(): Constructor

Slots

methy: a ModBamFiles data.frame specifying the samples and paths to bam files.
samples: the data.frame of sample annotation containing at least columns sample and group.
exons: the data.frame of exon information containing at least columns gene_id, chr, strand, start, end, transcript_id and symbol.
mod_code: the modification code of interest.