getDomainInflections: A wrapper function to generate a GRanges object of chromatin...

In biobenkj/compartmentalizer: Higher-order chromatin domain inference in single samples from methylation arrays and single cells from scRNA-seq and scATAC-seq

A wrapper function to generate a GRanges object of chromatin domain inflection points

Description

A wrapper function to generate a GRanges object of chromatin domain inflection points

Usage

getDomainInflections(
  gr,
  what = "score",
  res = 1e+06,
  chrs = c(paste0("chr", 1:22), "chrX"),
  genome = c("hg19", "hg38", "mm9", "mm10")
)

Arguments

gr	Input GRanges object with mcols column corresponding to chromatin domains
what	The name of the column containing the chromatin domain information
res	What resolution the domains were called
chrs	Which chromosomes to work on
genome	Which genome does the input data come from

Value

A GRanges object of compartment inflection points

Examples

data("k562_scrna_chr14", package = "compartmap")
chr14_domains <- scCompartments(k562_scrna_chr14,
                                res = 1e6, genome = "hg19",
                                group = TRUE, bootstrap = FALSE)
chr14_domain_inflections <- getDomainInflections(chr14_domains, what = "pc")

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