Nanopore Methylation Result

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 class 'NanoMethResult'
methy(object)

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

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

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

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

# S4 method for class '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)
#> Successfully matched 6 samples between data and annotation.
#> An object of class "NanoMethResult"
#> Slot "methy":
#> [1] "/home/runner/work/_temp/Library/NanoMethViz/methy_subset.tsv.bgz"
#> 
#> Slot "samples":
#> # A tibble: 6 × 2
#>   sample             group
#>   <chr>              <fct>
#> 1 B6Cast_Prom_1_bl6  bl6  
#> 2 B6Cast_Prom_1_cast cast 
#> 3 B6Cast_Prom_2_bl6  bl6  
#> 4 B6Cast_Prom_2_cast cast 
#> 5 B6Cast_Prom_3_bl6  bl6  
#> 6 B6Cast_Prom_3_cast cast 
#> 
#> Slot "exons":
#> # A tibble: 303 × 7
#>    gene_id chr   strand     start       end transcript_id symbol
#>    <chr>   <chr> <chr>      <int>     <int>         <int> <chr> 
#>  1 12189   chr11 -      101551769 101551879         92234 Brca1 
#>  2 12189   chr11 -      101549015 101549113         92234 Brca1 
#>  3 12189   chr11 -      101539981 101540034         92234 Brca1 
#>  4 12189   chr11 -      101535528 101535605         92234 Brca1 
#>  5 12189   chr11 -      101533939 101534027         92234 Brca1 
#>  6 12189   chr11 -      101532020 101532159         92234 Brca1 
#>  7 12189   chr11 -      101530992 101531094         92234 Brca1 
#>  8 12189   chr11 -      101529791 101529836         92234 Brca1 
#>  9 12189   chr11 -      101528001 101528077         92234 Brca1 
#> 10 12189   chr11 -      101523325 101526639         92234 Brca1 
#> # ℹ 293 more rows
#> 

x <- load_example_nanomethresult()
#> Successfully matched 6 samples between data and annotation.
methy(x)
#> [1] "/home/runner/work/_temp/Library/NanoMethViz/methy_subset.tsv.bgz"