非模式物种的注释

Posted 2021-02-03 djx571

一句话：我们经常会面对非模式物种的GO或者KEGG富集与注释。

1、载入我们所需要的包

if("clusterProfiler" %in% rownames(installed.packages()) == FALSE) {source("http://bioconductor.org/biocLite.R");biocLite("clusterProfiler")}
biocLite("colorspace")
suppressMessages(library(clusterProfiler))
ls("package:clusterProfiler")

library(AnnotationHub)
library(biomaRt)
library(enrichGO)

 2、收索目标物种

hub <- AnnotationHub::AnnotationHub()
query(hub, "Apis cerana")

 

3、抓取目标OrgDb

Apis_cerana.OrgDb <- hub[["AH62635"]]
columns(Apis_cerana.OrgDb)
Apis_cerana.OrgDb

 

4、抓取目标OrgDb

 

keys(Apis_cerana.OrgDb)
head(keys(Apis_cerana.OrgDb,keytype = "SYMBOL")) # 查看注释信息的symbol
hainan_genelist =read.table(‘C:/Users/djx/Desktop/海南.txt‘,header=TRUE,sep=‘	‘)
head(hainan_genelist)
colnames(hainan_genelist)
rownames(hainan_genelist)

bitr(keys(Apis_cerana.OrgDb)[15], ‘SYMBOL‘, c("ENTREZID","REFSEQ", "GO", "ONTOLOGY"), Apis_cerana.OrgDb)

hainan_geneid=as.character(hainan_genelist$Gene.ID)
hainan_geneid[1]
str(hainan_geneid)
rm(hainan_geneid)

sample_genes <- keys(Apis_cerana.OrgDb)[1:100]

hainan_enrich.go = enrichGO(sample_genes,
                        OrgDb        = Apis_cerana.OrgDb,
                        keyType      = ‘ENTREZID‘,
                        #ont= "BP",
                        pvalueCutoff = 0.05,
                        qvalueCutoff = 0.1,
                        readable     = T)