R/yeastCorrelatedExpression.R

In dtenenba/AdvancedR_stage5: Yeast Correlation Finder

correlationFinder <- function(dataFile, cor.threshold = 0.85) {
  tbl <- read.table(dataFile, sep='\t', header=T, quote='',
    comment.char='', fill=T, stringsAsFactors=FALSE)
  rownames (tbl) <- tbl$X
  exclude.these.columns <-  which(sapply (1:ncol (tbl),
  function(col) class (tbl [,col])) != 'numeric')
  if (length (exclude.these.columns) > 0)
    tbl <- tbl [, -exclude.these.columns]
  mtx.cor <- cor (t (as.matrix (tbl)), use='pairwise.complete.obs')
  mtx.cor <- upper.tri (mtx.cor) * mtx.cor

  max = nrow (mtx.cor)
  correlated.genes <- list()
  ret <- list()
  for (r in 1:max) {
    zz = as.integer (which (mtx.cor [r,] > cor.threshold))
    if (length (zz) > 0) {
      gene.a = rownames(mtx.cor) [r]
      genes.b = rownames(mtx.cor) [zz]
      correlated.genes[[gene.a]] <- genes.b
      ret[[ rownames(mtx.cor)[r] ]] <-
        rownames(mtx.cor)[zz]
      } # if length
     } # for r

  ret

} # correlationFinder