Map genes to chromosomal location for T2WEB

Script

file<-read.table(input_file, header=TRUE, sep="\t")


library("biomaRt")
#select ensembl
 entrez_ids<-file[,gene_ids_column]
ensembl = useMart("ensembl")
#select human
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)

##Had to split it in 3 parts, otherwise biomart couldnt handle big gene lists
biomart_1<-getBM(attributes = c("entrezgene","hgnc_symbol", "strand", "chromosome_name", "start_position","end_position", "transcript_start","transcript_end"), filters = "entrezgene", values = entrez_ids[1:round(length(entrez_ids)/3)], mart = ensembl)
biomart_2<-getBM(attributes = c("entrezgene","hgnc_symbol", "strand", "chromosome_name", "start_position","end_position", "transcript_start","transcript_end"), filters = "entrezgene", values = entrez_ids[(round(length(entrez_ids)/3)+1):round(length(entrez_ids)/1.5)], mart = ensembl)
biomart_3<-getBM(attributes = c("entrezgene","hgnc_symbol", "strand", "chromosome_name", "start_position","end_position", "transcript_start","transcript_end"), filters = "entrezgene", values = entrez_ids[(round(length(entrez_ids)/1.5)+1):length(entrez_ids)], mart = ensembl)

biomart<-rbind(biomart_1,biomart_2,biomart_3)
write.table(biomart,file_biomart, col.names=TRUE, row.names=FALSE,sep="\t")

R Server