diff --git a/R/correlationMatrix.R b/R/correlationMatrix.R
index 1e980ee9f6c9d1b57849d14ad225e273736accea..4f3db962ec732402d6fcdbc1bf498496c7cf4b30 100644
--- a/R/correlationMatrix.R
+++ b/R/correlationMatrix.R
@@ -162,7 +162,7 @@ getGenoCorMatrix <- function(lrsid, lchr, lpos, lrefall, pop, path = NULL, web =
         }
         testMat <- changeCoding(testMat, as.character(lrefall) == genoMap$REF)
         colnames(testMat) <- lind
-        cormat = stats::cor(t(testMat))
+        cormat = stats::cor(t(testMat), use = "complete.obs")
         if (pruning) {
             return(pruneCorMatrix(cormat, rthresh))
         }