enrichReactome {signatureSearch} | R Documentation |
Reactome Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched Reactome pathways with FDR control from hypergeometric test.
enrichReactome( gene, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2, universe, minGSSize = 5, maxGSSize = 500, readable = FALSE )
gene |
a vector of entrez gene id. |
organism |
one of "human", "rat", "mouse", "celegans", "yeast", "zebrafish", "fly". |
pvalueCutoff |
Cutoff value of pvalue. |
pAdjustMethod |
one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
qvalueCutoff |
Cutoff value of qvalue |
universe |
background genes |
minGSSize |
minimal size of genes annotated by functional term for testing. |
maxGSSize |
maximal size of each gene set for analyzing |
readable |
TRUE or FALSE indicating whether to convert gene Entrez ids to gene Symbols in the 'itemID' column in the FEA result table. |
A feaResult
instance.
# This method supports duplicated elements in "gene" gene <- c(rep("4312",4), rep("8318",2), "991", "10874") #data(geneList, package="DOSE") #rc <- enrichReactome(gene=gene, universe=names(geneList)) #result(rc)