NanoMethResult-class {NanoMethViz} | R Documentation

## 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'
    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 containg 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-method`: methylation data path getter.

- `methy<-,NanoMethResult-method`: methylation data path setter.

- `samples,NanoMethResult-method`: sample annotation getter.

- `samples<-,NanoMethResult,data.frame-method`: sample annotation setter.

- `exons,NanoMethResult-method`: exon annotation getter.

- `exons<-,NanoMethResult,data.frame-method`: exon annotation getter.

### 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")
    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)

[Package NanoMethViz version 2.0.0 Index]