enrichKEGG2 {signatureSearch} | R Documentation |
Given a vector of gene identifiers, this function returns KEGG pathway enrichment results based on a hypergeometric test with duplication support in the test set.
enrichKEGG2( gene, organism = "hsa", keyType = "kegg", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, minGSSize = 5, maxGSSize = 500, qvalueCutoff = 0.2, readable = FALSE )
gene |
a vector of entrez gene ids (here the test set) |
organism |
supported organism are listed in http://www.genome.jp/kegg/catalog/org_list.html |
keyType |
one of "kegg", 'ncbi-geneid', 'ncbi-proteinid' or 'uniprot' |
pvalueCutoff |
pvalue cutoff |
pAdjustMethod |
one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
universe |
background genes |
minGSSize |
minimal size of genes annotated by ontology term for testing. |
maxGSSize |
maximal size of genes annotated for testing |
qvalueCutoff |
qvalue cutoff |
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.
# Method supports duplicated elements in "gene", which should be entrez ids gene <- c(rep("4312",4), rep("8318",2), "991", "10874") #data(geneList, package="DOSE") #kk <- enrichKEGG2(gene = gene, universe=names(geneList)) #head(kk)