Pairwise Comparison of Rows in R

Question

I have a dataset that contains results for many tests across many samples. The samples are replicated within the dataset. I would like to compare the test results between replic

Answer 1

You are on the right track with t(combn(nrow(data),2)). See below for how I would do it.

testCols <- which(grepl("^Test\\d+",colnames(data)))

TestsCompare=function(x,y){
  ##how many non-NA values overlap
  overlaps <- sum(!is.na(x) & !is.na(y))
  ##of those that overlap, how many match
  matches <- sum(x==y, na.rm=T)
  ##of those that overlap, how many do not match
  non_matches <- overlaps - matches # complement of matches
  c(overlaps,matches,non_matches)
}

RowCompare= function(x){
  comp <- NULL
  pairs <- t(combn(nrow(x),2))
  for(i in 1:nrow(pairs)){
    row_a <- pairs[i,1]
    row_b <- pairs[i,2]
    a_tests <- x[row_a,testCols]
    b_tests <- x[row_b,testCols]
    comp <- rbind(comp, c(row_a, row_b, TestsCompare(a_tests, b_tests)))
  }
  colnames(comp) <- c("row_a","row_b","overlaps","matches","non_matches")
  return(comp)
}

out = lapply(data.split, RowCompare)

Produces:

> out
$Sample1
     row_a row_b overlaps matches non_matches
[1,]     1     2        8       6           2

$Sample2
     row_a row_b overlaps matches non_matches
[1,]     1     2       10       9           1
[2,]     1     3        9       8           1
[3,]     2     3        9       9           0