ensembl id to gene symbol
2
0
Entering edit mode
5.1 years ago
krushnach80 ★ 1.0k

I have output from Deseq2 but those genes names are ENSEMBL id , I need the gene name . Can any one help me how do i map the ENSEMBL id to gene name ? Sample code or something I read about biomart tried their code given in manual but i could make it work use annotaiondbi but i get this error Error in .testForValidKeys(x, keys, keytype, fks) : None of the keys entered are valid keys for 'ENSEMBL'. Please use the keys method to see a listing of valid arguments.

Any suggestion or help would be highly appreciated

R Ensembl • 4.2k views
ADD COMMENT
2
Entering edit mode

You should provide entire code snippet that you are using along with R package name etc. Just posting an error message without any other information is not enough. Please edit the original post and add this information there.

ADD REPLY
1
Entering edit mode

When your ENSEMBL gene ids contain a decimal point org.Hs.eg.db will complain this. Remove those decimal point from ENSEMBL gene id and do, it will work. I did this like an hour before.

ADD REPLY
2
Entering edit mode
5.1 years ago
  1. Download gene ID and symbols from biomart
  2. In R:

_

library("dplyr")  # You might have to install this
annotated = left_join(your_results, what_you_got_from_biomart, by=c(DESeq_column_name == biomart_column_name))
ADD COMMENT
0
Entering edit mode

so it would match on its own ?I mean I have filtered out results which I dont want so it would be a problem i suppose .I donr have to make query to the Biomart data base..!!

ADD REPLY
1
Entering edit mode

You'd query biomart outside of R. Sure, you could do it inside too, but it'd be faster to just make a few clicks with the mouse and save a file.

Yes, the left_join() function joins two data frames on one or more common columns. It handles cases of missing data and multiple matches and is much much much faster than the built in match() function that comes with R. If you're not familiar with the dplyr package, I would recommend reading through its vignette, it's an incredibly useful package and one of the core components of the "tidyverse".

ADD REPLY
2
Entering edit mode
5.1 years ago

Today I had this problem, and since Ensmbl is temporary offline, I got some suggestion which fitted my problem, hopes it does to you. https://biodbnet-abcc.ncifcrf.gov/db/db2dbRes.php Cheers, me.

ADD COMMENT

Login before adding your answer.

Traffic: 1379 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6