I have a data.frame containing Ensembl IDs in one column; I would like to find corresponding gene symbols for the values of that column and add them to a new column in my data frame. I used bioMaRt but It couldn't find any of the Ensembl IDs!
Here is my sample data (df[1:2,]
):
row.names organism gene
41 Homo-Sapiens ENSP00000335357
115 Homo-Sapiens ENSP00000227378
and I want to get something like this
row.names organism gene id
41 Homo-Sapiens ENSP00000335357 CDKN3
115 Homo-Sapiens ENSP00000227378 HSPA8
and here is my code:
library('biomaRt')
mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl"))
genes <- df$genes
df$id <- NA
G_list <- getBM(filters= "ensembl_gene_id", attributes= c("ensembl_gene_id",
"entrezgene", "description"),values=genes,mart= mart)
Then I get this when I check the G_list
[1] ensembl_gene_id entrezgene description <0 rows> (or 0-length row.names)
So I couldn't add G_list to my df! because there is nothing to add!
Thanks in Advance,