Description Usage Arguments Value Author(s) See Also Examples
View source: R/enrichPathway.R
Pathway Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enriched pathways with FDR control.
1 2 3 4 5 6 7 8 9 10 11 | 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
1 2 3 4 5 6 7 | 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)
|
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