gene symbol not showing for ensembl gene ids using biomart
I have a list of esembl gene ids from RNA-seq experiment and i want to get their corresponding ref-seq ids and gene symbols but the gene symbol not showing. I may be doing something wrong, could you please take a look at my code?
#load library
library(biomaRt)
ids <- c("ENSMUSG00000047180", "ENSMUSG00000025964", "ENSMUSG00000012187", "ENSMUSG00000055980", "ENSMUSG00000034220",
"ENSMUSG00000026463","ENSMUSG00000026688", "ENSMUSG00000015090", "ENSMUSG00000026879", "ENSMUSG00000027254")
#map ensembl gene ids to ref-seq ids and show gene symbols
mart <- biomaRt::useMart(biomart = "ENSEMBL_MART_ENSEMBL",
dataset = "mmusculus_gene_ensembl",
host = "https://www.ensembl.org")
genes <- getBM(filters = "ensembl_gene_id", attributes = c("hgnc_symbol", "refseq_mrna"), values = ids, mart = mart)
We can see that corresponding gene symbols are missing from resulting query
> genes
hgnc_symbol refseq_mrna
1 NA
2 NA NM_026713
3 NA NM_008963
4 NA NM_011780
5 NA NM_001167949
6 NA NM_213616
7 NA NM_025569
8 NA NM_001362945
9 NA NM_001362947
10 NA NM_001362948
11 NA NM_001206367
12 NA NM_001206368
13 NA NM_001206369
14 NA NM_146120
15 NA NM_032393
16 NA NM_001173506
17 NA NM_016696
18 NA NM_153408
19 NA NM_010570
1 answer
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Hi, try "entrezgene_accession" instead of "hgnc_symbol" in attributes vector for getting gene symbol
Awwww! thank you all (@seidel @Ben_Ensembl @mohammadhassanj) for your help :)
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