preprocessArrays: Preprocess arrays for compartment inference

In biobenkj/compartmap: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

Preprocess arrays for compartment inference

Description

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 (require(minfiData)) {
  grSet <- mapToGenome(ratioConvert(preprocessNoob(RGsetEx.sub)))
  preprocessArrays(grSet)
} 

biobenkj/compartmap documentation built on Oct. 18, 2023, 11:11 a.m.