scCompartments: Estimate A/B compartments from ATAC-seq data

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

Description

getATACABsignal returns estimated A/B compartments from ATAC-seq data.

Usage

scCompartments(
  obj,
  res = 1000000,
  parallel = TRUE,
  chr = NULL,
  targets = NULL,
  cores = 2,
  bootstrap = TRUE,
  num.bootstraps = 1000,
  genome = c("hg19", "hg38", "mm9", "mm10"),
  group = FALSE,
  assay = c("atac", "bisulfite", "rna")
)

Arguments

obj	Input SummarizedExperiment object
res	Compartment resolution in bp
parallel	Whether to run samples in parallel
chr	What chromosome to work on (leave as NULL to run on all chromosomes)
targets	Samples/cells to shrink towards
cores	How many cores to use when running samples in parallel
bootstrap	Whether we should perform bootstrapping of inferred compartments
num.bootstraps	How many bootstraps to run
genome	What genome to work on ("hg19", "hg38", "mm9", "mm10")
group	Whether to treat this as a group set of samples
other	Another arbitrary genome to compute compartments on

Value

A RaggedExperiment of inferred compartments

Examples

data("groupATAC_raw_filtered_chr14", package = "compartmap")
sc_compartments <- scCompartments(filtered.data.chr14, parallel=F, chr="chr14", bootstrap=F, genome="hg19")

JordanVeldboom/compartmap documentation built on July 3, 2020, 6:32 p.m.