getATACABsignal {compartmap} | R Documentation |
getATACABsignal
returns estimated A/B compartments from methylation array data.
getATACABsignal(obj, res = 1e+06, parallel = FALSE, allchrs = FALSE, chr = NULL, targets = NULL, ...)
obj |
Input GenomicRatioSet object |
res |
Compartment resolution (in bp) |
parallel |
Should the inference be done in parallel? |
allchrs |
Whether all autosomes should be used for A/B inference |
chr |
Specify a chromosome to analyze |
targets |
Specify samples as shrinkage targets |
... |
Additional arguments |
This function estimates A/B compartments shrinking towards a global mean of targets or across samples
A p x n matrix (samples as columns and compartments as rows) of compartments
library(GenomicRanges) library(SummarizedExperiment) library(Homo.sapiens) data(bulkATAC_raw_filtered_chr14, package = "compartmap") atac_compartments <- getATACABsignal(filtered.data.chr14, chr = "chr14", genome = "hg19")