hi
I got a list of Entrez IDs after converting probe IDs. Now, I want Gene symbols and name from those Entrez IDs.
Can anyone suggest some function in R, which can help this?
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written
by
parinv •
1 answer
library(biomaRt)
## change your dataset if necessary below
mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
## return data.frame of all genes with both their entrez ids and gene symbols (some genes have no entrez id)
dataframe.genes <- getBM(attributes=c("entrezgene_id","external_gene_name"), values=my.genes, mart=mart)
I fixed it already now you get everything
Thank you, I used given code with small changes: gene<-getBM(attributes = c("entrezgene_id","external_gene_name"), values = rownames(Ra_mod), mart=mart)
and i got results: entrezgene_id external_gene_name
1 NA MT-TF
2 NA MT-RNR1
3 NA MT-TV
4 NA MT-RNR2
5 NA MT-TL1
6 4535 MT-ND1
how do I check if its correct?
That is still the unfiltered data.frame.
You would need to include: filters="entrez_gene_id" in your getBM() call for it to only use your ids.
thank you for your suggestion.
But after adding this filter, the sequence of the IDs changed. I want them in the original sequence (list). Can you suggest how to do it? -And also the number of IDs decreased compared to the original list. What can be the reason for that?
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Did you try searching?
yes, I read all these posts, but nothing seems to be working.
"nothing seems to be working" is not helpful, please provide the codes you have tried together with errors/warnings.