Question

I’m doing an experiment where I have “regions” with some associated statistic (actually many other statistics and descriptive columns), and a comma-separated list of genes that lie in those regions. This list will be variable in number, and may not contain anything (“NA”).

How can I “melt” table a:

  region_id  statistic      genelist
          1        2.5       A, B, C
          2        0.5    B, C, D, E
          3        3.2          <NA>
          4        0.1          E, F

To create another table with a separate entry for each gene in the list of genes? I.e.

   region_id statistic gene
           1       2.5    A
           1       2.5    B
           1       2.5    C
           2       0.5    B
           2       0.5    C
           2       0.5    D
           2       0.5    E
           3       3.2 <NA>
           4       0.1    E
           4       0.1    F

I’m guessing there’s a way to do this with R/plyr, but I’m not sure how. Thanks in advance.

Edit:

Using R you can recreate these toy vectors with this code:

a <- structure(list(region_id = 1:4, statistic = c(2.5, 0.5, 3.2, 
0.1), genelist = structure(c(1L, 2L, NA, 3L), .Label = c("A, B, C", 
"B, C, D, E", "E, F"), class = "factor")), .Names = c("region_id", 
"statistic", "genelist"), class = "data.frame", row.names = c(NA, 
-4L))

b <- structure(list(region_id = c(1L, 1L, 1L, 2L, 2L, 2L, 2L, 3L, 
4L, 4L), statistic = c(2.5, 2.5, 2.5, 0.5, 0.5, 0.5, 0.5, 3.2, 
0.1, 0.1), gene = structure(c(1L, 2L, 3L, 2L, 3L, 4L, 5L, NA, 
5L, 6L), .Label = c("A", "B", "C", "D", "E", "F"), class = "factor")), .Names = c("region_id", 
"statistic", "gene"), class = "data.frame", row.names = c(NA, 
-10L))

Answer 1

There are a few ways to do it. This way works, although there may be better ways…

library(stringr) # for str_split
join(subset(a, select=c("region_id", "statistic")), 
     ddply(a, .(region_id), summarise, gene=str_split(genelist, ",\\S*")[[1]]))

Needs plyr and stringr loaded.

Oh, here’s a better way:

ddply(a, .(region_id), 
      function(x) data.frame(gene=str_split(x$genelist, ",\\S*")[[1]], 
                             statistic=x$statistic))