Hi, I am trying to convert Ensembl id of lincRNA to its symbol (gene name) by using biomaRt in R, but the dataset doesn't give me a proper annotation. I know that Ensembl has the annotation for this lincRNA, since I can see it on IGV. For your information, I used GRCh38. p13 annotation from GENCODE when I mapped the reads.
I simplified my code as much as possible just to see if the biomaRt provides me a proper annotation for the lincRNA gene, but it gives me NA.
library(biomaRt) fix_name <- as.character("lincRNA_id") mart <- useDataset("hsapiens_gene_ensembl", useMart("ensembl")) symbol <- getBM(filters = "ensembl_gene_id", attributes = c("ensembl_gene_id","hgnc_symbol"), values = fix_name, mart = mart) >symbol ensembl_gene_id hgnc_symbol 1 lincRNA_id NA
Could you please let me know how I can get the gene name from the id? I am new to bioinformatics, so any help is much appreciated. Thank you