rChEA3 (version 0.2.0)

queryChEA3: Query ChEA3 API for TF enrichment

Description

#' Sends a gene list to the ChEA3 web service to identify enriched transcription factors using multiple evidence sources. The gene list should consist of HGNC-approved gene symbols.

Usage

queryChEA3(genes, query_name = "rChEA3_query", verbose = TRUE)

Value

A named list of data frames. Each element corresponds to a ChEA3 collection and contains an enrichment table with transcription factors and their statistics. The expected names are: c("Integrated--meanRank", "Integrated--topRank", "GTEx--Coexpression", "ARCHS4--Coexpression", "ENCODE--ChIP-seq", "ReMap--ChIP-seq", "Literature--ChIP-seq", "Enrichr--Queries").

Arguments

genes

Character vector of HGNC gene symbols.

query_name

Optional query name (default: "rChEA3_query").

verbose

Logical; if TRUE, print a grouped summary of available result collections (default: TRUE).

Examples

# \donttest{
    results <- queryChEA3(c("SMAD9","FOXO1","MYC","STAT1","STAT3","SMAD3"))
    names(results)
    head(results[["Integrated--meanRank"]])
# }