enrichGO2 {signatureSearch} | R Documentation |
Given a vector of gene identifiers, this function returns GO term enrichment results based on a hypergeometric test with duplication support in the test set.
enrichGO2( gene, OrgDb, keytype = "SYMBOL", ont = "MF", pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2, minGSSize = 5, maxGSSize = 500, pool = FALSE )
gene |
a vector of gene SYMBOL ids (here the test set) |
OrgDb |
OrgDb |
keytype |
Gene ID type of test set |
ont |
One of "MF", "BP", "CC" or "ALL" |
pvalueCutoff |
pvalue cutoff |
pAdjustMethod |
one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
universe |
background genes |
qvalueCutoff |
qvalue cutoff |
minGSSize |
minimum size of each gene set in annotation system |
maxGSSize |
maximum size of each gene set in annotation system |
pool |
If ont='ALL', whether 3 GO ontology should be combined |
A feaResult
instance.
# The method supports duplicated elements in 'gene', # which should be gene SYMBOL ids for GO term enrichment. gene <- c(rep("HDAC1",4), rep("HDAC3",2), "SOX8", "KLK14") # data(targetList) # ego <- enrichGO2(gene = gene, OrgDb="org.Hs.eg.db", ont="MF", # universe=names(targetList))