tissue_by_celltype_enrichment {scMappR}

tissue_by_celltype_enrichment

Description

This function uses a Fisher's-exact-test to rank gene-set enrichment.

Usage

tissue_by_celltype_enrichment(
  gene_list,
  species,
  name = "CT_Tissue_example",
  p_thresh = 0.05,
  rda_path = "",
  isect_size = 3,
  return_gmt = FALSE
)

Arguments

gene_list

A character vector of gene symbols with the same designation (e.g. mouse symbol - mouse, human symbol - human) as the gene set database.

species

Species of cell-type marker to use ('human' or 'mouse').

name

Name of the pdf to be printed.

p_thresh

The Fisher's test cut-off for a cell-marker to be enriched.

rda_path

Path to a .rda file containing an object called "gmt". Either human or mouse cell-type markers split by experiment. If the correct file isn't present they will be downloaded from https://github.com/wilsonlabgroup/scMappR_Data.

isect_size

Number of genes in your list and the cell-type.

return_gmt

Return .gmt file – recommended if downloading from online as it may have updated (T/F).

Details

Complete a Fisher's-exact test of an input list of genes against one of the two curated tissue by cell-type marker datasets from scMappR.

Value

List with the following elements:

enriched

Data frame of enriched cell-types from tissues.

gmt

Cell-markers in enriched cell-types from tissues.

Examples

data(POA_example)
POA_generes <- POA_example$POA_generes
POA_OR_signature <- POA_example$POA_OR_signature
POA_Rank_signature <- POA_example$POA_Rank_signature
Signature <- POA_Rank_signature
rowname <- get_gene_symbol(Signature)
rownames(Signature) <- rowname$rowname
genes <- rownames(Signature)[1:100]

enriched <- tissue_by_celltype_enrichment(gene_list = genes, 
species = "mouse",p_thresh = 0.05, isect_size = 3)