scCompartments: Estimate A/B compartments from single-cell sequencing data

View source: R/scCompartments.R

scCompartmentsR Documentation

Estimate A/B compartments from single-cell sequencing data

Description

scCompartments returns estimated A/B compartments from sc-seq data.

Usage

scCompartments(
  obj,
  res = 1e+06,
  parallel = FALSE,
  chr = NULL,
  targets = NULL,
  cores = 2,
  bootstrap = TRUE,
  num.bootstraps = 100,
  genome = c("hg19", "hg38", "mm9", "mm10"),
  group = FALSE,
  assay = c("atac", "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

assay

What type of single-cell assay is the input data ("atac" or "rna")

Value

A RaggedExperiment of inferred compartments

Examples

data("k562_scrna_chr14", package = "compartmap")
sc_compartments <- scCompartments(k562_scrna_chr14, parallel=FALSE, chr="chr14", bootstrap=FALSE, genome="hg19")

biobenkj/compartmentalizer documentation built on Oct. 13, 2023, 5:26 p.m.