[R] applying wilcox.test to every combination of rows in a matrix (pairwise)

[debra ragland]

Hello All,

I have written the following loop which will apply/split the same vector of numbers (pc1.eigv) to each (logical) row of a matrix and run a wilcox.test on those values that line up with TRUE and those that line up with FALSE. It works fine. However, I am now interested in using the same vector and (logical)matrix run the wilcox.test only this time I would like information about pairs of rows (not just single rows as it already does).

The loop:
n.iteration=dim(as.matrix(p))[1]
n.test= rep(NA, n.iteration )
for( i in 1:n.iteration ){  ## i=1
i_spl<-split(pc1.eigv, p[i,])
if( sum(p[i,])==15 | sum(p[i,])==0) { n.test[i]=NA  }
if( sum(p[i,])!=15 & sum(p[i,])!=0) { 
testout=wilcox.test(i_spl$'TRUE', i_spl$'FALSE')
n.test[i]=testout$p.value     }
}


some sample data
p<-matrix(c(rep(c(F,T,F),3), rep(c(T,F,T),3), rep(c(T,T,F),3), rep(c(F,F,T),3)))

pc1.eigv<-runif(4, 1.0, 2.0)

After some searching I thought that perhaps the combn function would help me (i.e. combn(p)) for the same loop but I get an error.

Can anyone help with this?