I have a list of genes (n = 5726) for which I wanted to get the chrom, start and end. I used the following query:
library(biomaRt) ensembl <- useMart("ensembl", dataset = "hsapiens_gene_ensembl") lit.genes.ann <- getBM(attributes = c('chromosome_name','start_position','end_position','hgnc_symbol'), filters = 'hgnc_symbol', values = gene.names, mart = ensembl)
I got results for all but 79 genes back. This list was probably generated some time back and I am using the current ensembl build to get the data. I looked up one such gene EMR1 on Genecards and looks like it has been changed to ADGRE1.
Is there a way to do a batch search & import to get current HGNC symbols for all the obsolete genes that I have? I am not looking for all the aliases but just one approved HGNC symbol per obsolete gene name. Some of the gene names are:
ACN9 AQPEP BAI1 PAPL EMR1