Gene Ontology using clusterProfiler

Question

[adR]

Hi Dear friends, I just love to take your few minutes for the following question, please!

Maybe it is an easy question but I am doing it for the first time and don't know how I can deal with it. I was converting my gene symbols to ENTREZID using clusterProfiler and got the following warning.

Warning message:
In bitr(rownames(muscleFG_genes), fromType = "SYMBOL", toType = c("ENTREZID",  :
  9.61% of input gene IDs are fail to map...

Therefore, how can correct these genes to be mapped into ENTREZID? Thank you so much! Best, AD

Answer 1

[Vasu]

data <- c("FAP","COL10A1","ADAM12","POSTN")

library(clusterProfiler)
library(org.Hs.eg.db)
### Convert UpReg Gene symbols to Ensembl ids and Entrez ids
Ent_Ensem_UNI <- bitr(data, fromType = "SYMBOL",
                       toType = c("ENTREZID", "ENSEMBL", "UNIPROT"),
                       OrgDb = org.Hs.eg.db)

>  Ent_Ensem_UNI

    SYMBOL ENTREZID         ENSEMBL    UNIPROT
1      FAP     2191 ENSG00000078098     B4DLR2
2      FAP     2191 ENSG00000078098     Q12884
3  COL10A1     1300 ENSG00000123500     Q03692
4   ADAM12     8038 ENSG00000148848     U5NE98
5   ADAM12     8038 ENSG00000148848     O43184
6   ADAM12     8038 ENSG00000148848     A8K6G4
8    POSTN    10631 ENSG00000133110 A0A024RDT5
9    POSTN    10631 ENSG00000133110     Q15063
10   POSTN    10631 ENSG00000133110     B1ALD9
11   POSTN    10631 ENSG00000133110 A0A024RDS2