compute_gene_scores: Compute gene counts

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

Compute gene counts

Description

Aggregate gene-level scores across all bootstrap iterations.

• boot: Mean specificity of all genes within a given cell type.

• hit: Mean specificity of a hit gene within a given cell type.

Usage

compute_gene_scores(
  sct_data,
  annotLevel,
  bootstrap_list = NULL,
  hits,
  combinedGenes,
  reps = NULL,
  exp_mats = NULL,
  return_hit_exp = FALSE,
  verbose = TRUE
)

Arguments

sct_data	List generated using generate_celltype_data.
annotLevel	An integer indicating which level of sct_data to analyse (Default: 1).
bootstrap_list	The output of get_summed_proportions_iterate.
hits	list of gene names. The target gene set.
reps	Number of random gene lists to generate (Default: 100, but should be >=10,000 for publication-quality results).
return_hit_exp	Return the expression of each hit gene.
verbose	Print messages.

Value

data.table

NathanSkene/EWCE documentation built on April 10, 2024, 1:02 a.m.