Preprocess arrays for compartment inference

Preprocess arrays for compartment inference

Usage

preprocessArrays(
  obj,
  genome = c("hg19", "hg38", "mm9", "mm10"),
  other = NULL,
  array.type = c("hm450", "EPIC")
)

Arguments

obj

Input SummarizedExperiment

genome

What genome are we working on ("hg19", "hg38", "mm9", "mm10")

other

Another arbitrary genome to compute compartments on

array.type

What type of array is this ("hm450", "EPIC")

Value

A preprocessed SummarizedExperiment to compute compartments

Examples

if (requireNamespace("minfiData", quietly = TRUE)) {
  grSet <- minfi::preprocessNoob(minfiData::RGsetEx.sub) |>
    minfi::ratioConvert() |>
    minfi::mapToGenome()
  preprocessArrays(grSet)
}
#> Loading required package: IlluminaHumanMethylation450kmanifest
#> Loading required package: minfi
#> Loading required package: Biostrings
#> Loading required package: XVector
#> 
#> Attaching package: ‘Biostrings’
#> The following object is masked from ‘package:base’:
#> 
#>     strsplit
#> Loading required package: bumphunter
#> Loading required package: foreach
#> Loading required package: iterators
#> Loading required package: parallel
#> Loading required package: locfit
#> locfit 1.5-9.12 	 2025-03-05
#> Error in h(simpleError(msg, call)): error in evaluating the argument 'object' in selecting a method for function 'mapToGenome': error in evaluating the argument 'object' in selecting a method for function 'ratioConvert': invalid class “MethylSet” object: superclass "ExpData" not defined in the environment of the object's class