How to convert a value of columnA to a value of columnB (in R)?

Question

[kelly.wang135]

Hi all,

I am having a trouble using R. I want to make a function for converting IDs between two ID formats using R.

From the file (below),

"idConverion.txt"

gene_name gene_id

AB ENSG001

ABC ENSG002

WER ENSG0052

and the function I defined below,

geneConv <- function(input, output) {

df <- fread("idConversion.txt")

input <- df$gene_name

output <- df$gene_id

return(output)

}

I want to get this result.

geneConv("AB")

"ENSG001"

But with this function, I could only get all of the IDs of column B. Could someone help me with this?

Answer 1

[cpad0112]

Replace test.txt with input.txt.

library(data.table)
geneConv <- function(x) {
    df <- fread("test.txt")
    output=df[gene_name==x,.(gene_id)]
    return(output)
}
geneConv("AB")

See if you can take fread function out. This is because every time, you want to search a gene ID, it has to execute fread and this affects the performance. Try something like this:

df <- fread("test.txt")
geneConv <- function(x) {
    output=df[gene_name==x,.(gene_id),nomatch=NA]
    return(output)
}

however, I would suggest to use this:

geneConv <- function(x) {
+     output=df[gene_name %in% x ,.(gene_id)]
+     return(output)
+     }
> 
> geneConv(c("AB","CD","ABC"))
   gene_id
1: ENSG001
2: ENSG002