enrichMKEGG: KEGG Module Enrichment Analysis of a gene set. Given a vector...
In aiminy/ModifiedclusterProfiler: statistical analysis and visualization of functional profiles for genes and gene clusters
Description
Usage
Arguments
Value
Description
KEGG Module Enrichment Analysis of a gene set.
Given a vector of genes, this function will return the enrichment KEGG Module
categories with FDR control.
Usage
1
2
3
enrichMKEGG(gene, organism = "hsa", keyType = "kegg", pvalueCutoff = 0.05,
pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500,
qvalueCutoff = 0.2)
Arguments
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
Cutoff value of pvalue.
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
Value
A enrichResult instance.
aiminy/ModifiedclusterProfiler documentation built on May 10, 2019, 7:37 a.m.
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Description Usage Arguments Value
Description
KEGG Module Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG Module categories with FDR control.
Usage
1 2 3 | enrichMKEGG(gene, organism = "hsa", keyType = "kegg", pvalueCutoff = 0.05,
pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500,
qvalueCutoff = 0.2)
|
Arguments
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 |
Cutoff value of pvalue. |
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 |
Value
A enrichResult instance.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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