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

The pairwise.wilcox.test function seems like it would be useful here; perhaps like this?

out <- lapply(2:6, function(x) pairwise.wilcox.test(d[[x]], d$group))
names(out) <- names(d)[2:6]
out

If you just want the p-values, you can go through and extract those and make a matrix.

sapply(out, function(x) {
    p <- x$p.value
    n <- outer(rownames(p), colnames(p), paste, sep='v')
    p <- as.vector(p)
    names(p) <- n
    p
})
##         var1      var2      var3 var4      var5
## 2v1 0.5414627 0.8205958 0.4851572    1 1.0000000
## 3v1 0.1778222 0.3479835 1.0000000    1 1.0000000
## 2v2        NA        NA        NA   NA        NA
## 3v2 0.5414627 0.3479835 0.3784941    1 0.6919826

Also note that pairwise.wilcox.test adjusts for multiple comparisons using the Holm method; if you'd rather do something different, look at the p.adjust parameter.