test_spot_enrichment: perform enrichment testing based on differential gene...

In tmirus/TTT: What the Package Does (One Line, Title Case)

Description

perform enrichment testing based on differential gene expression analysis

Usage

test_spot_enrichment(
  analysis.data,
  counts,
  db_dataset = "mmusculus_gene_ensembl",
  gene_id = "hgnc",
  ncores = 4,
  mirror = NULL
)

Arguments

analysis.data	output of analyze_clustering
counts	numeric non-negativ matrix containing gene expression for all spots (spots x genes)
db_dataset	ensembl dataset to use. default "mmusculus_gene_ensembl" (mouse), for human data use "hsapiens_gene_ensembl"
gene_id	character denoting the gene symbols to use; default "hgnc" for HGNC symbols; use "ensembl" for ensembl gene ids
ncores	integer > 0, number of cores to use
mirror	string indicating ensembl mirror site; must be one of "standard", "uswest", "useast", "asia"; default is "standard"

Value

list containing two entries:

1. enrichments - matrix contining p-values of enrichments test for each spot and GO term enriched in at least one spot(terms x spots)
   

2. term.names - character vector containing full names of the GO ids in the enrichment matrix

tmirus/TTT documentation built on April 17, 2021, 11:04 p.m.