enstoncbi_convert.R

  ##If using for the first time, source the below packages

# source("https://bioconductor.org/biocLite.R")
# biocLite("org.Mm.eg.db")

##Load the db to the environment

library("org.Mm.eg.db")

## The list of EnsEMBL Gene IDs are stored in a file "ens.txt". Read the text file as a table

my.ensmusg <- read.table("ens.txt", 
                       sep="\n", 
                       col.names=c("gene_id"), 
                       fill=FALSE, 
                       strip.white=TRUE)

## Convert the table to chr

my.ensmusg1 <- sapply(my.ensmusg,as.character)

## Check for the existence of the gene in the NCBI db
a <- sapply(my.ensmusg1, function(x) exists(x, org.Mm.egENSEMBL2EG))


## Select the gene available
my.ensmusg.existed <- my.ensmusg1[a]


## Convert entire db to a list and choose the required gene_ids
xx <- as.list(org.Mm.egENSEMBL2EG)
out <- xx[my.ensmusg.existed]


## Write the output to a file temporarily and read it back as table variable. Direct trail to trnaspose out variable didn't work

write.table(out,"tmp.csv",sep=",")
tmp <- read.csv("tmp.csv",fill=FALSE,strip.white=TRUE)

## Take a transpose of the data
t_tmp <- t(tmp)


## Write the final output to a file. 
write.table(t_tmp,"out_gene_id.csv",sep=",")