UPDATE: I posted another question with more details that is related to this problem. The biostar link can be found here :link
I am using
library(org.Hs.eg.db)
I have a list of human gene symbols like this
mysymbols<-c("AXUD1", "CENTG1", "DGCR14", "ERBB2IP", "KIAA1627", "NARG1L", "NOS2A", "O00366", "Q6ZP10")
I want to get the entrez id for these genes and these are all aliases so I am using
info4gene = select(org.Hs.eg.db, mysymbols, c("ENTREZID"), "ALIAS")
to get the entrez ids. This is able to get the entrez ids for some of the gene symbols. The output I get is like this
ALIAS ENTREZID
1 AXUD1 64651
2 CENTG1 116986
3 DGCR14 8220
4 ERBB2IP 55914
5 KIAA1627 <NA>
6 NARG1L 79612
7 NOS2A 4843
8 O00366 <NA>
9 Q6ZP10 <NA>
So for example KIAA1627 is an alias for the METTL14 gene and the result should return 57721 instead of NA. I have tried other things like using the mygene python library and bitr function from cluster profiler library. Also I would like to do this process automatically so I need a script or a code rather than the ncbi website or the online david tool.
what is
select
? what is that library ?i am using library(org.Hs.eg.db)
Not sure if this is applicable. Worth a mention: mapping between gene symbol and entrez ID
unfortunately not. I am using the same function mentioned in that post. But as my output shows I can't get the gene id for all of the gene symbols with this method. I also tried "SYMBOL" instead of "ALIAS" but no result.