geneEnrich: Perform functional enrichment on a set of genes.

In Bin-Chen-Lab/octad_desktop: Open Cancer TherApeutic Discovery (OCTAD)

Description

Perform functional enrichment analysis for disease signature genes. This function interacts with Enrichr's REST API for enrichment analysis. Databases are specified with underscores for spaces (e.g. "WikiPathways_2016", "KEGG_2019_Human", "GO_Biological_Process_2018"). Other databases are listed on the website (https://amp.pharm.mssm.edu/Enrichr/#stats). A list of data.frame is produced. Every data.frame contain enriched terms for a specific selected database.

Usage

geneEnrich(gene_list=NULL,
                       database_list=NULL,output=FALSE)

Arguments

gene_list	a vector of HGNC gene symbols.
database_list	a vector of EnrichR-supported databases.
output	if TRUE dataframe with names of selected databases with GO will be produced.

Value

GO_enriched

list with result of GO analysis. Every leaf is a data.frame containing GO enrichment for specific database.

See Also

diffExp

Examples

#gene list
genes=c('PHF14', 'RBM3', 'MSL1', 'PHF21A', 'ARL10', 'INSR', 'JADE2', 'P2RX7')
db=c('KEGG_2019_Human','KEGG_2015')
enrich=geneEnrich(gene_list=genes,database_list=db)
#output
gene_e = geneEnrich(genes,  database_list = db)
dim(gene_e$KEGG_2019_Human)
dim(gene_e$GO_Biological_Process_2017)

Bin-Chen-Lab/octad_desktop documentation built on Oct. 28, 2020, 11:13 a.m.