ID转换

setwd("D:/R/R-4.0.5/bin/project_fuxian/4-TCGA")
suppressMessages(library(clusterProfiler)) 
suppressMessages(library("org.Hs.eg.db")) 
load("DEG_matrix_DESeq.Rdata")

nrDEG <- DESeq2_DEG
colnames(nrDEG)[c(2,5)] <- c("logFC","P.Value")

logFC_cutoff <- with(nrDEG,mean(abs(logFC)+2*sd(abs(logFC))))
#logFC_cutoff <- 1.2
nrDEG$change <- as.factor(with(nrDEG,ifelse(P.Value < 0.01 & abs(logFC) > logFC_cutoff,
                                  ifelse(logFC > logFC_cutoff,"up","down"),"not")))
table(nrDEG$change)

## 
##  down   not    up 
##   865 29776   737

keytypes(org.Hs.eg.db)

##  [1] "ACCNUM"       "ALIAS"        "ENSEMBL"      "ENSEMBLPROT"  "ENSEMBLTRANS"
##  [6] "ENTREZID"     "ENZYME"       "EVIDENCE"     "EVIDENCEALL"  "GENENAME"    
## [11] "GO"           "GOALL"        "IPI"          "MAP"          "OMIM"        
## [16] "ONTOLOGY"     "ONTOLOGYALL"  "PATH"         "PFAM"         "PMID"        
## [21] "PROSITE"      "REFSEQ"       "SYMBOL"       "UCSCKG"       "UNIGENE"     
## [26] "UNIPROT"

library(stringr)
rownames(nrDEG) <- substr(rownames(nrDEG),1,15)
nrDEG$ENSEMBL <- rownames(nrDEG)
#ID转换
df <- bitr(rownames(nrDEG),fromType = "ENSEMBL",toType = c("ENTREZID"),OrgDb = org.Hs.eg.db)

## 'select()' returned 1:many mapping between keys and columns

## Warning in bitr(rownames(nrDEG), fromType = "ENSEMBL", toType = c("ENTREZID"), :
## 29.23% of input gene IDs are fail to map...

head(df)

##           ENSEMBL ENTREZID
## 1 ENSG00000175063    11065
## 3 ENSG00000115163     1058
## 4 ENSG00000161888   147841
## 5 ENSG00000088325    22974
## 6 ENSG00000075218    51512
## 7 ENSG00000137225    11131