remove(goterm) continue # remove top level # GO:0003674 molecular_function # GO:0005575 cellular_component # GO:0008150 biological_process all_goterm_obj_list = [obofile.query_term(go_term) for go_term in all_goterm_list if go_term != "GO:0003674" and go_term != "GO:0005575" and...
> head(keys(org.Hs.eg.db,keytype = "GO")) [1] "GO:0002576" "GO:0003674" "GO:0005576" "GO:0005615" "GO:0008150" "GO:0031093" 3、select函数返回需要的注释数据 # select(annopkg, keys, columns, keytype) # annopkg是注释包;keys是ID号;columns是想得到的列;keytype是使用的key的类型 >...
gene_list <- godata[["GO:0008150"]] # 获取与生物学过程相关的基因 您还可以使用其他函数来获取与其他GO术语相关的基因,比如与分子功能(GO:0003674)或细胞组分(GO:0005575)相关的基因。 2. 如何在R语言中使用下载的GO基因集进行基因功能注释? 在R语言中,您可以使用下载的GO基因集进行基因功能注释,以了解基...
1 1 GO:0002576 TAS BP 2 1 GO:0003674 ND MF 3 1 GO:0005576 IDA CC 1. 2. 3. 4. 5. 6. 7. 8. 9. 10. 这里的代码只是根据Entrez ID 得到了GO注释信息,其实这个R包也包含了gene symbol, ensembl id等很多其他的基因ID。 许多做富集分析的包就会从物种对应...
(org.Hs.eg.db, keytype = "ENTREZID")[1:3] > select(org.Hs.eg.db, keys = k, columns = c("GO", "ONTOLOGY"), keytype="ENTREZID") 'select()' returned 1:many mapping between keys and columns ENTREZID GO EVIDENCE ONTOLOGY 1 1 GO:0002576 TAS BP 2 1 GO:0003674 ND MF 3 1 ...
# 导入必要的库library(GOplot)library(org.Hs.eg.db)# 模拟数据genes<-c("Gene1","Gene2","Gene3","Gene4")go_annotations<-list(Gene1=c("GO:0008150","GO:0003674"),Gene2=c("GO:0008150","GO:0005575"),Gene3=c("GO:0008150","GO:0003674"),Gene4=c("GO:0005575"))# 进行GO富集分析...
(geneID2go_list)## $`1`## [1] "GO:0002576" "GO:0003674" "GO:0005576" "GO:0005576" "GO:0005615"## [6] "GO:0008150" "GO:0031012" "GO:0031093" "GO:0034774" "GO:0043312"## [11] "GO:0070062" "GO:0072562" "GO:1904813"library(topGO)goID2gene_list <- inverseList(geneID2go...
>k<-keys(org.Hs.eg.db,keytype="ENTREZID")[1:3]>select(org.Hs.eg.db,keys=k,columns=c("GO","ONTOLOGY"),keytype="ENTREZID")'select()'returned1:many mapping between keys and columnsENTREZIDGOEVIDENCEONTOLOGY11GO:0002576TASBP21GO:0003674NDMF31GO:0005576IDACC ...
>k<-keys(org.Hs.eg.db,keytype="ENTREZID")[1:3]>select(org.Hs.eg.db,keys=k,columns=c("GO","ONTOLOGY"),keytype="ENTREZID")'select()'returned1:many mapping between keys and columnsENTREZIDGOEVIDENCEONTOLOGY11GO:0002576TASBP21GO:0003674NDMF31GO:0005576IDACC ...
1、gene2go:第一列为基因ID(GID),第二列为GO条目(GO), 第三列为IEA(EVIDENCE) 。括号里是列名 原始的格式是:基因1/GO1,GO2,GO3,...GOn,如下图 需要整理为: 基因1/GO1 ... 基因1/GOn 例: SoffiXsponR570.01Ag000100 GO:0003674 SoffiXsponR570.01Ag000100 GO:0005096 ...