getCompartments: Estimate A/B compartments

In compartmap: A/B compartment inference from ATAC-seq and methylation array data

Description

getCompartments returns estimated A/B compartments from ATAC-seq and methylation array data

Usage

getCompartments(obj, type = c("atac", "array"), res = 1e+06,
  parallel = FALSE, chrs = "chr1", genome = "hg19", targets = NULL,
  run_examples = FALSE, ...)

Arguments

obj	The object with which to perform compartment inference
type	The type of data that obj represents (e.g. atac or array)
res	Resolution of compartments in base pairs (default is 1e6)
parallel	Should the estimates be done in parallel (default is FALSE)
chrs	Chromosomes to operate on (can be individual chromosomes, a list of chromosomes, or all)
genome	Genome to use (default is hg19)
targets	Specify samples to use as shrinkage targets
run_examples	Whether to run ATAC-seq and 450k example analysis
...	Other parameters to pass to internal functions

Details

This is a wrapper function to perform A/B compartment inference. Compartmentalizer implements a Stein estimator to shrink per-sample compartment estimates towards a global mean. The expected input for this function can be generated using packages like SeSAMe and ATACseeker.

Value

A p x n matrix (samples as columns and compartments as rows) to pass to embed_compartments

Examples

library(GenomicRanges)
library(SummarizedExperiment)
library(Homo.sapiens)

#ATAC-seq data
data(bulkATAC_raw_filtered_chr14, package = "compartmap")
atac_compartments <- getCompartments(filtered.data.chr14, type = "atac", parallel = FALSE, chrs = "chr14")
## Not run: 
#450k data
data(meth_array_450k_chr14, package = "compartmap")
array_compartments <- getCompartments(array.data.chr14, type = "array", parallel = FALSE, chrs = "chr14")
## End(Not run)

compartmap documentation built on Nov. 8, 2020, 5:34 p.m.