enrichPathway {ReactomePA} | R Documentation |
Pathway Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched pathways with FDR control.
enrichPathway( gene, organism = "human", pvalueCutoff = 0.05, pAdjustMethod = "BH", qvalueCutoff = 0.2, universe, minGSSize = 10, 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 Ontology term for testing. |
maxGSSize |
maximal size of each geneSet for analyzing |
readable |
whether mapping gene ID to gene Name |
A enrichResult
instance.
Guangchuang Yu http://ygc.name
gene <- c("11171", "8243", "112464", "2194", "9318", "79026", "1654", "65003", "6240", "3476", "6238", "3836", "4176", "1017", "249") yy = enrichPathway(gene, pvalueCutoff=0.05) head(summary(yy)) #plot(yy)