Description Usage Arguments Value Author(s) See Also Examples
KEGG Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.
1 2 3 4 5 6 7 8 9 10 11 12 | enrichKEGG(
gene,
organism = "hsa",
keyType = "kegg",
pvalueCutoff = 0.05,
pAdjustMethod = "BH",
universe,
minGSSize = 10,
maxGSSize = 500,
qvalueCutoff = 0.2,
use_internal_data = FALSE
)
|
gene |
a vector of entrez gene id. |
organism |
supported organism listed in 'http://www.genome.jp/kegg/catalog/org_list.html' |
keyType |
one of "kegg", 'ncbi-geneid', 'ncib-proteinid' and 'uniprot' |
pvalueCutoff |
adjusted pvalue cutoff on enrichment tests to report |
pAdjustMethod |
one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none" |
universe |
background genes. If missing, the all genes listed in the database (eg TERM2GENE table) will be used as background. |
minGSSize |
minimal size of genes annotated by Ontology term for testing. |
maxGSSize |
maximal size of genes annotated for testing |
qvalueCutoff |
qvalue cutoff on enrichment tests to report as significant. Tests must pass i) |
use_internal_data |
logical, use KEGG.db or latest online KEGG data |
A enrichResult
instance.
Guangchuang Yu http://guangchuangyu.github.io
enrichResult-class
, compareCluster
1 2 3 4 |
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