An S4 class to manage epiRomics databases and downstream results

The epiRomicsS4 class holds a genomic annotation set along with the metadata needed to interpret it (data-source catalog, TxDb identifier, organism annotation package, genome assembly). Every slot is exposed through a public getter and setter — users should access slot contents through those accessors rather than obj@slot or methods::slot(obj, "slot").

Value

An S4 class definition for epiRomicsS4

Slots

annotations

GRanges object containing genomic annotations. Access via annotations().

meta

data.frame containing metadata about loaded data sources. Access via meta().

txdb

character string of TxDb package::object name. Access via txdb().

organism

character string of org.db package name. Access via organism().

genome

character string of genome assembly name (e.g., 'mm10', 'hg38'). Access via genome().

See also

Public accessors for this class: annotations, annotations<-, meta, meta<-, txdb, txdb<-, organism, organism<-, genome, genome<-. Overview: epiRomicsS4-accessors.

Examples

showClass("epiRomicsS4")
#> Class "epiRomicsS4" [package "epiRomics"]
#> 
#> Slots:
#>                                                                   
#> Name:  annotations        meta        txdb    organism      genome
#> Class:     GRanges  data.frame   character   character   character
db <- make_example_database()
genome(db)
#> [1] "hg38"
organism(db)
#> [1] "org.Hs.eg.db"
length(annotations(db))
#> [1] 24