Map genes to chromosomal location

None

library("biomaRt")
#select ensembl
 entrez_ids<-file[,gene_ids_column]
ensembl = useMart("ensembl")
#select human
ensembl = useDataset("hsapiens_gene_ensembl",mart=ensembl)
#biomart<-getBM(attributes = c("entrezgene","hgnc_symbol", "strand", "chromosome_name", "start_position","end_position", "transcript_start","transcript_end"), filters = "entrezgene", values = entrez_ids, mart = ensembl)

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)
output_file_biom<- paste("genes_on_chromosome",Sys.time(),".txt",sep="")
write.table(biomart,output_file_biom, col.names=TRUE, row.names=FALSE,sep="\t")

file_biomart<-output_file_biom

print("biomart calling done")

Name	Description
input_file	the input gene file with entrez gene ids, that will be mapped to the genome
gene_ids_column	This input parameter indicates the column of the input file where the entrez gene ids are stored
working_directory	the desired working directory. This workflow saves the results in .txt files and therefore its useful for the user to provide a directory to save the results in.

Source	Sink
gene_ids_column	map_to_chr_location:gene_ids_column
input_file	read_files:input_file
working_directory	read_files:directory
map_to_chr_location:file_biomart	mapped_file_biomart

Map genes to chromosomal location

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