ModBamResult-class: Modbam methylation results

In Shians/NanoMethViz: Visualise methylation data from Oxford Nanopore sequencing

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.

Shians/NanoMethViz documentation built on Dec. 17, 2024, 8:56 a.m.