NanoMethResult-class: Nanopore Methylation Result

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

Nanopore Methylation Result

Description

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

Usage

NanoMethResult(methy, samples, exons = NULL)

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

## S4 replacement method for signature 'NanoMethResult,ANY'
methy(object) <- value

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

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

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

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

Arguments

methy	the path to the methylation tabix file.
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.
object	the NanoMethResult object.
value	the exon annotation.

Value

a NanoMethResult object to be used with plotting functions

the path to the methylation data.

the sample annotation.

the exon annotation.

Functions

• NanoMethResult(): Constructor

• methy(NanoMethResult): methylation data path getter.

• methy(object = NanoMethResult) <- value: methylation data path setter.

• samples(NanoMethResult): sample annotation getter.

• samples(object = NanoMethResult) <- value: sample annotation setter.

• exons(NanoMethResult): exon annotation getter.

• exons(object = NanoMethResult) <- value: exon annotation setter.

Slots

methy

the path to the methylation tabix file.

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.

Examples

methy <- system.file(package = "NanoMethViz", "methy_subset.tsv.bgz", mustWork = FALSE)
sample <- c(
    "B6Cast_Prom_1_bl6",
    "B6Cast_Prom_1_cast",
    "B6Cast_Prom_2_bl6",
    "B6Cast_Prom_2_cast",
    "B6Cast_Prom_3_bl6",
    "B6Cast_Prom_3_cast"
)
group <- c(
    "bl6",
    "cast",
    "bl6",
    "cast",
    "bl6",
    "cast"
)
sample_anno <- data.frame(sample, group, stringsAsFactors = FALSE)
exon_tibble <- get_example_exons_mus_musculus()
NanoMethResult(methy, sample_anno, exon_tibble)

x <- load_example_nanomethresult()
methy(x)

Shians/NanoMethViz documentation built on Oct. 11, 2024, 7:17 a.m.