How to apply the wilcox.test to a whole dataframe in R?

Question

I have a data frame with one grouping factor (the first column) with multiple levels (more than two) and several columns with data. I want to apply the wilcox.test

Answer 1

Updating my answer to work across columns

test.fun <- function(dat, col) { 

 c1 <- combn(unique(dat$group),2)
 sigs <- list()
 for(i in 1:ncol(c1)) {
    sigs[[i]] <- wilcox.test(
                   dat[dat$group == c1[1,i],col],
                   dat[dat$group == c1[2,i],col]
                 )
    }
    names(sigs) <- paste("Group",c1[1,],"by Group",c1[2,])

 tests <- data.frame(Test=names(sigs),
                    W=unlist(lapply(sigs,function(x) x$statistic)),
                    p=unlist(lapply(sigs,function(x) x$p.value)),row.names=NULL)

 return(tests)
}


tests <- lapply(colnames(dat)[-1],function(x) test.fun(dat,x))
names(tests) <- colnames(dat)[-1]
# tests <- do.call(rbind, tests) reprints as data.frame

# This solution is not "slow" and outperforms the other answers significantly: 
system.time(
  rep(
   tests <- lapply(colnames(dat)[-1],function(x) test.fun(dat,x)),10000
  )
)

#   user  system elapsed 
#  0.056   0.000   0.053 

And the result:

tests

$var1
                Test  W          p
1 Group 1 by Group 2 28 0.36596737
2 Group 1 by Group 3 39 0.05927406
3 Group 2 by Group 3 38 0.27073136

$var2
                Test    W         p
1 Group 1 by Group 2 19.0 0.8205958
2 Group 1 by Group 3 36.5 0.1159945
3 Group 2 by Group 3 40.5 0.1522726

$var3
                Test    W         p
1 Group 1 by Group 2 13.0 0.2425786
2 Group 1 by Group 3 23.5 1.0000000
3 Group 2 by Group 3 41.0 0.1261647

$var4
                Test  W         p
1 Group 1 by Group 2 26 0.4323470
2 Group 1 by Group 3 30 0.3729664
3 Group 2 by Group 3 29 0.9479518

$var5
                Test    W         p
1 Group 1 by Group 2 24.0 0.7100968
2 Group 1 by Group 3 19.0 0.5324295
3 Group 2 by Group 3 17.5 0.2306609