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[annotation] clusterProfiler包

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发表于 2018-9-13 10:47:56 | 显示全部楼层 |阅读模式
1)enrichGO:(GO富集分析)
描述:GO Enrichment Analysis of a gene set. Given a vector of genes, this function will return the enrichment GO categories after FDR control
语法:
enrichGO(gene, OrgDb, keyType = "ENTREZID", ont = "MF",pvalueCutoff = 0.05, pAdjustMethod = "BH", universe, qvalueCutoff = 0.2,
minGSSize = 10, maxGSSize = 500, readable = FALSE, pool = FALSE)
参数介绍:
gene:a vector of entrez gene id.
OrgDb:OrgDb
keyType:keytype of input gene
ont:One of "MF", "BP", and "CC" subontologies.
pvalueCutoff:Cutoff value of pvalue.
pAdjustMethod:one of "holm", "hochberg", "hommel", "bonferroni", "BH", "BY", "fdr", "none"
universe:background genes
qvalueCutoff:qvalue cutoff
minGSSize:minimal size of genes annotated by Ontology term for testing.
maxGSSize:maximal size of genes annotated for testing
readable:whether mapping gene ID to gene Name
pool:If ont=’ALL’, whether pool 3 GO sub-ontologies
举例:
[Python] 纯文本查看 复制代码
data(geneList, package = "DOSE")
de <- names(geneList)[1:100]
yy <- enrichGO(de, 'org.Hs.eg.db', ont="BP", pvalueCutoff=0.01)
head(yy)


2)KEGG Enrichment(KEGG富集分析)
描述:Analysis of a gene set. Given a vector of genes, this function will return the enrichment KEGG categories with FDR control.
语法:
enrichKEGG(gene, organism = "hsa", keyType = "kegg", pvalueCutoff = 0.05,
           pAdjustMethod = "BH", universe, minGSSize = 10, maxGSSize = 500,
           qvalueCutoff = 0.2, use_internal_data = FALSE)
参数:
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
use_internal_data
logical:use KEGG.db or latest online KEGG data
举例:
[Python] 纯文本查看 复制代码
data(geneList, package='DOSE')
de <- names(geneList)[1:100]
yy <- enrichKEGG(de, pvalueCutoff=0.01)
head(yy


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