R_IDmapping

#How to map gene names to NCBI gene identifiers 

#First, install biomaRt package and create a "mart" item
library(biomaRt)
mart <- useMart("ensembl")

#Optional - how to identify datasets and attributes
#datasets <- listDatasets(mart)
#attributes = listAttributes(ensembl)

#Define an "ensembl" item which contains the datasets and attributes you want to use
ensembl <- useEnsembl(biomart = "genes", dataset = "hsapiens_gene_ensembl")

#Create a dataframe of hsa genes with 2 attributes 
Ensembl_hsa_genes <- getBM(attributes = c("external_gene_name","entrezgene_id"),mart = useMart("ensembl", dataset = "hsapiens_gene_ensembl"))

#Change column name to be able to merge that list with the original list of genes you want the IDs for
colnames(Ensembl_hsa_genes) <-c('GeneTarget','NCBIID')
head(Ensembl_hsa_genes)

#merge the two lists by adding the Ensembl list to the original dataset
GeneTargets3E <- merge(GeneTargets3, Ensembl_hsa_genes, by="GeneTarget")