@@ -131,14 +131,31 @@ discordantRun <- function(v1, v2, x, y = NULL, transform = TRUE,

         for(i in 1:iter) {

             # make sure pairs are independent

             rowIndex <- sample(nrow(x), subSize)

-            colIndex <- sample(nrow(y), subSize)

-            mat1 <- matrix(v1, nrow = nrow(x), byrow = FALSE)

-            mat2 <- matrix(v2, nrow = nrow(x), byrow = FALSE)

-            subSampV1 <- sapply(1:subSize, function(x) mat1[rowIndex[x], 

-                                                            colIndex[x]])

-            subSampV2 <- sapply(1:subSize, function(x) mat2[rowIndex[x], 

-                                                            colIndex[x]])

+            if(is.null(y)) {

+              # colIndex <- sample(nrow(x), subSize)

+              sampleNames <- rownames(x)

+              

+              if (floor(length(sampleNames) / 2) < subSize) {

+                warning("Provided subSize too high. Using number of features divided by 2.")

+                subSize <- floor(length(sampleNames) / 2)

+              }

+              

+              nameSet1 <- sample(sampleNames, subSize)

+              nameSet2 <- setdiff(sampleNames, nameSet1)

+              nameSetA <- paste0(nameSet1, "_", nameSet2)

+              nameSetB <- paste0(nameSet2, "_", nameSet1)

+              subSampV1 <- ifelse(is.na(v1[nameSetA]), v1[nameSetB], v1[nameSetA])

+              subSampV2 <- ifelse(is.na(v2[nameSetA]), v2[nameSetB], v2[nameSetA])

+            } else {

+              colIndex <- sample(nrow(y), subSize)

+              mat1 <- matrix(v1, nrow = nrow(x), byrow = FALSE)

+              mat2 <- matrix(v2, nrow = nrow(x), byrow = FALSE)

+              subSampV1 <- sapply(1:subSize, function(x) mat1[rowIndex[x], 

+                                                              colIndex[x]])

+              subSampV2 <- sapply(1:subSize, function(x) mat2[rowIndex[x], 

+                                                              colIndex[x]])

+            }

             sub.pdata <- cbind(subSampV1, subSampV2)

             sub.class <- cbind(.assignClass(subSampV1, param1, components),

@@ -265,6 +282,10 @@ em.normal.partial.concordant <- function(data, class, components) {

   return(rtn)

 }

+# .createSubsamples <- function(x, y = NULL, v1, v2) {

+#   

+# }

+

 # Internal function to validate user inputs for discordantRun()

 #' @importFrom methods is

 .checkDiscordantInputs <- function(v1, v2, x, y, transform, 

@@ -290,6 +311,9 @@ em.normal.partial.concordant <- function(data, class, components) {

   }

 }

+# Internal function that checks whether all types of component are present

+#   in given vectors. If a certain component is not present, we run into a

+#   divide-by-zero error that crashes R

 .checkForMissingComponents <- function(zx, zy) {

   sumZx <- colSums(zx)

   sumZy <- colSums(zy)