News: Ensembl 93 is out!
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gravatar for amonida
15 months ago by
amonida20
United Kingdom
amonida20 wrote:

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

ADD COMMENTlink written 15 months ago by amonida20

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 REPLYlink written 14 months ago by cagenet3420
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