Question

I have a long list e2i, which “maps” rownames to values, and has duplicate rownames:

> head(e2i)
$`679594`
[1] "IPR019956"

$`679594`
[1] "IPR019954"

$`679594`
[1] "IPR019955"

$`679594`
[1] "IPR000626"

$`682397`
[1] "IPR019956"

$`682397`
[1] "IPR019954"

I need to convert it into a list with unique rownames, where each named element would be a list of (either named or unnamed) values:

> str(mylist)
List of 2
 $ 679594:List of 3
  ..$ : chr "IPR019956"
  ..$ : chr "IPR019954"
  ..$ : chr "IPR019955"
 $ 682397:List of 2
  ..$ : chr "IPR019956"
  ..$ : chr "IPR019954"

I believe there’s a short and elegant solution.

As for long and ugly solution – I think I could do that with a loop like this:

mytest = function(e2i) {
    result = list()
    for (e in names(e2i)) {
            # iterate all rownames, including duplicates
            if (e %in% names(result)) {
                    # convert existing element to a list (if not already a list),
                    # then append new value e2i[[e]] to that nested list
            }
            else {
                    # just add the value to the result
                    result = c(result, e2i[[e]])
            }
    }
    return(result)
}

Initially data was in a matrix, and for my loop solution draft above I’d use it as input:

> head(entrez2interpro_matrix)
  EntrezGene.ID Interpro.ID
1        679594   IPR019956
2        679594   IPR019954
3        679594   IPR019955
4        679594   IPR000626
5        682397   IPR019956
6        682397   IPR019954

Answer 1

Have you looked at the reshape package?

Or just use unstack():

> d
  EntrezGene.ID Interpro.ID
1        679594   IPR019956
2        679594   IPR019954
3        679594   IPR019955
4        679594   IPR000626
5        682397   IPR019956
6        682397   IPR019954
> unstack(d, Interpro.ID ~ EntrezGene.ID)
$`679594`
[1] "IPR019956" "IPR019954" "IPR019955" "IPR000626"

$`682397`
[1] "IPR019956" "IPR019954"