generate_controlled_bootstrap_geneset

Used to generated cell type-controlled bootstrapped gene sets.

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.

Value

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

Details

See controlled_geneset_enrichment for examples.