check_controlled_args: check_controlled_args

In NathanSkene/EWCE: Expression Weighted Celltype Enrichment

check_controlled_args

Description

Check the input arguments of the controlled_geneset_enrichment.

Usage

check_controlled_args(
  bg,
  sct_data,
  annotLevel,
  disease_genes,
  hits,
  functional_genes,
  funcGenes,
  combinedGenes
)

Arguments

bg	List of gene symbols containing the background gene list (including hit genes). If bg=NULL, an appropriate gene background will be created automatically.
sct_data	List generated using generate_celltype_data.
annotLevel	An integer indicating which level of sct_data to analyse (Default: 1).
disease_genes	Array of gene symbols containing the disease gene list. Does not have to be disease genes. Must be from same species as the single cell transcriptome dataset.
hits	Hit genes.
functional_genes	Array of gene symbols containing the functional gene list. The enrichment of this gene set within the disease_genes is tested. Must be from same species as the single cell transcriptome dataset.
funcGenes	functional_genes that are within combinedGenes.
combinedGenes	sct_data genes that are in the background bg.

Value

Null output.

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