bootstrapCompartments: Non-parametric bootstrapping of compartments and...

View source: R/bootstrapCompartments.R

bootstrapCompartmentsR Documentation

Non-parametric bootstrapping of compartments and summarization of bootstraps/compute confidence intervals

Description

Non-parametric bootstrapping of compartments and summarization of bootstraps/compute confidence intervals

Usage

bootstrapCompartments(
  obj,
  original.obj,
  bootstrap.samples = 1000,
  chr = "chr14",
  assay = c("rna", "atac", "array"),
  parallel = TRUE,
  cores = 2,
  targets = NULL,
  res = 1e+06,
  genome = c("hg19", "hg38", "mm9", "mm10"),
  q = 0.95,
  svd = NULL,
  group = FALSE,
  bootstrap.means = NULL
)

Arguments

obj

List object of computed compartments for a sample with 'pc' and 'gr' as elements

original.obj

The original, full input SummarizedExperiment of all samples/cells

bootstrap.samples

How many bootstraps to run

chr

Which chromosome to operate on

assay

What sort of assay are we working on

parallel

Whether to run the bootstrapping in parallel

cores

How many cores to use for parallel processing

targets

Targets to shrink towards

res

The compartment resolution

genome

What genome are we working on

q

What sort of confidence intervals are we computing (e.g. 0.95 for 95 percentCI)

svd

The original compartment calls as a GRanges object

group

Whether this is for group-level inference

bootstrap.means

Pre-computed bootstrap means matrix

Value

Compartment estimates with summarized bootstraps and confidence intervals

Examples

  
# this needs a good example


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