generate_controlled_bootstrap_geneset: generate_controlled_bootstrap_geneset

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

generate_controlled_bootstrap_geneset

Description

Used to generated cell type-controlled bootstrapped gene sets.

Usage

generate_controlled_bootstrap_geneset(
  hits,
  sct_data,
  annotLevel,
  reps,
  controlledCT = FALSE,
  verbose = TRUE
)

Arguments

hits	List of gene symbols containing the target gene list. Will automatically be converted to human gene symbols if geneSizeControl=TRUE.
sct_data	List generated using generate_celltype_data.
annotLevel	An integer indicating which level of sct_data to analyse (Default: 1).
reps	Number of random gene lists to generate (Default: 100, but should be >=10,000 for publication-quality results).
controlledCT	[Optional] If not NULL, and instead is the name of a cell type, then the bootstrapping controls for expression within that cell type.
verbose	Print messages.

Details

See controlled_geneset_enrichment for examples.

Value

Matrix of genes (such that nrows=length(hits) and ncols=reps), where each column is a gene list.

NathanSkene/EWCE documentation built on Nov. 3, 2024, 8:16 a.m.