tissue_by_celltype_enrichment: tissue_by_celltype_enrichment
In DustinSokolowski/scMappR: Single Cell Mapper

Description Usage Arguments Details Value Examples

View source: R/tissue_by_celltype_enirchment.R

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

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

`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/DustinSokolowski/scMappR_Data.
`isect_size`	Number of genes in your list and the cell-type.
`return_gmt`	Return .gmt file – reccomended if downloading from online as it may have updated (T/F).

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.

List with the following elements:

`enriched`	Data frame of enriched cell-types from tissues.
`gmt`	Cell-markers in enriched cell-types from tissues.

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)