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
#> Loading required package: IlluminaHumanMethylation450kanno.ilmn12.hg19
#> Filtering to open sea CpG loci...
#> Converting to squeezed M-values.
#> class: GenomicRatioSet 
#> dim: 47 6 
#> metadata(0):
#> assays(3): Beta M CN
#> rownames(47): cg01003813 cg01051089 ... cg01757887 cg03930849
#> rowData names(0):
#> colnames(6): 5723646052_R02C02 5723646052_R04C01 ... 5723646053_R05C02
#>   5723646053_R06C02
#> colData names(13): Sample_Name Sample_Well ... Basename filenames
#> Annotation
#>   array: IlluminaHumanMethylation450k
#>   annotation: ilmn12.hg19
#> Preprocessing
#>   Method: NA
#>   minfi version: NA
#>   Manifest version: NA