precomputeBootstrapMeans: Pre-compute the global means for bootstrapping compartments

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

Pre-compute the global means for bootstrapping compartments

Description

Pre-compute the global means for bootstrapping compartments

Usage

precomputeBootstrapMeans(
  obj,
  targets = NULL,
  num.bootstraps = 100,
  assay = c("atac", "rna", "array"),
  parallel = FALSE,
  num.cores = 1
)

Arguments

obj	Input SummarizedExperiment object
targets	Optional targets to shrink towards
num.bootstraps	The number of bootstraps to compute
assay	What type of assay the data are from
parallel	Whether to run in parallel
num.cores	How many cores to use for parallel processing

Value

A matrix of bootstrapped global means

Examples

data("k562_scrna_chr14", package = "compartmap")
scrna.bootstrap.global.means <- precomputeBootstrapMeans(k562_scrna_chr14, assay = "rna", num.bootstraps = 2)

biobenkj/compartmap documentation built on Oct. 18, 2023, 11:11 a.m.