News:Ensembl 93 is out!
0
0
Entering edit mode
amonida ▴ 20
@amonida-7119
Last seen 12 months ago
United Kingdom

Dear all

The new Ensembl marts for release 93 are now live on www.ensembl.org.

If you are using biomaRt, you can change your host to access our most recent data:

ensembl_mart_93 <- useEnsembl(biomart=“ensembl")

You can find the complete list of the changes at http://www.ensembl.org/info/website/news.html

Thanks,

Amonida

ensembl mart ensembl93 biomart news News • 398 views
ADD COMMENT
0
Entering edit mode

Thank you .

Dear Amonida,

I'm using Biomart package after fferential expression analysis with DESeq2 package. I use ENSEMBL ID. After differential analysis I would like to obtain the HGNC symbol or VGNC symbol from ENSEMBL ID. The following function work for HGNC symbol but I failed to retrieve vgnc gene name.

add.anns <- function(df, mart, ...)
{
  nm <- rownames(df)
  anns <- getBM(
    attributes = c("ensembl_gene_id", "hgnc_symbol","vgnc_genename", "description"),
    filters = "ensembl_gene_id", values = nm, mart = mart)
  anns <- anns[match(nm, anns[, 1]), ]
  colnames(anns) <- c("ID", "Gene Symbol", "Gene Description")
  df <- cbind(anns, df[, 2:ncol(df)])
  rownames(df) <- nm
  df
  }

 

Can you  tell me if there is an attribute to obtain vgnc gene name because I failed to obtained it (didn't find it with listAttributes(mart) ) .

Thank you in advance.

By the way your url retrieves  "404 not found error".

Regards

Carine

ADD REPLY

Login before adding your answer.

Traffic: 426 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