scCompartments {compartmap} | R 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")

[Package compartmap version 1.10.0 Index]