2 1 GO:0003674 ND MF 3 1 GO:0005576 HDA CC 图3 AnnotationDbi和clusterProfiler同时加载select函数报错 GO提供的下载文件我没找到需要的信息,就不写了。
## GO:0005576 GO:0005576 extracellular region 3296 ## GO:0065010 GO:0065010 extracellular membrane-bounded organelle 2220 ## GO:0070062 GO:0070062 extracellular exosome 2220 ## GO:0044421 GO:0044421 extracellular region part 2941 ## enrichmentScore NES pvalue p.adjust qvalues ## GO:0031982 -0.2...
AI代码解释 >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 这里的代码只是根...
GO:0005576 extracellular reg ion 0,0454192 0,980568 0,0279238 6 GO:0008270 zinc ion binding 0,0458914 0,98194 0,0292415 34 posttranscriptional regulation of GO:0010608 gene expression 0,0480475 0,986095 0,030316 2 14 849 2752 under 14 849 2752 under ...
## GO:0005576 -0.2746489 -1.312485 0.001009082 0.03721229 0.02816364 ## GO:0065010 -0.2570342 -1.222048 0.001013171 0.03721229 0.02816364 ## GO:0070062 -0.2570342 -1.222048 0.001013171 0.03721229 0.02816364 ## GO:0044421 -0.2744658 -1.310299 0.001014199 0.03721229 0.02816364 ...
Category Term GOTERM_MF_FAT GO:0030594~neurotransmitter receptor activity GOTERM_CC_FAT GO:0005576~extracellular region GOTERM_MF_FAT GO:0042165~neurotransmitter binding GOTERM_MF_FAT GO:0008188~neuropeptide receptor activity GOTERM_MF_FAT GO:0042923~neuropeptide binding GOTERM_CC_FAT GO:0044421~...
topGO是一个专门用于做GO富集分析的R包,它默认从GO.db中读取GO的分类和结构信息,结合富集分析的结果,它可以画出如下所示的GO有向无环图
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的db包中读取GO注释信息。
GO::Parser - parses all GO files formats and types SYNOPSIS fetch GO::Model::Graph objects using a parser: # Scenario 1: Getting objects from a file use GO::Parser; my $parser = new GO::Parser({handler=>'obj',use_cache=>1}); ...
(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...