clusterProfiler包

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：

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：

data(geneList, package='DOSE')
de <- names(geneList)[1:100]
yy <- enrichKEGG(de, pvalueCutoff=0.01)
head(yy)