diff --git a/R/classifySex.R b/R/classifySex.R
index de3d0eb..dbbe779 100644
--- a/R/classifySex.R
+++ b/R/classifySex.R
@@ -65,7 +65,7 @@ classifySex<-function(x, genome=NULL, qc = TRUE)
 {
   # Perform some checks on the data
   if(is.null(x)) stop("Counts matrix missing")
-  x <- as.matrix(x)
+#  x <- as.matrix(x)
   if(is.null(genome)){
     message("Genome not specified. Human genome used. Options are 'Hs' for
         human and 'Mm' for mouse. We currently don't support other genomes.")
diff --git a/R/findMFDoublet.R b/R/findMFDoublet.R
index e8d04dd..8b0bd79 100644
--- a/R/findMFDoublet.R
+++ b/R/findMFDoublet.R
@@ -50,7 +50,7 @@ findMfDoublet<-function(x, genome=NULL, qc = FALSE)
 {
     # Perform some checks on the data
     if (is.null(x)) stop("Counts matrix missing")
-    x <- as.matrix(x)
+#    x <- as.matrix(x)
 
     if (is.null(genome)){
         message("Genome not specified. Human genome used. Options are 'Hs' for
diff --git a/R/lognormCounts.R b/R/lognormCounts.R
index cf01c24..96c1261 100644
--- a/R/lognormCounts.R
+++ b/R/lognormCounts.R
@@ -19,7 +19,7 @@ lognormCounts <- function(x, log = TRUE, prior.count = 0.5, lib.size)
   # Belinda Phipson
   # 26 February 2020
 {
-  x <- as.matrix(x)
+#  x <- as.matrix(x)
   #lib.size <- colSums(x)
   M <- median(lib.size)
   if(log){
diff --git a/R/preprocess.R b/R/preprocess.R
index 5719cfd..4fb915b 100644
--- a/R/preprocess.R
+++ b/R/preprocess.R
@@ -72,7 +72,7 @@
 #'
 preprocess<- function(x, genome=genome, qc=qc){
 
-    x <- as.matrix(x)
+#    x <- as.matrix(x)
     row.names(x)<- toupper(row.names(x))
     
     if (is.null(row.names(x))){
diff --git a/R/preprocessDb.R b/R/preprocessDb.R
index 0660694..250aac7 100644
--- a/R/preprocessDb.R
+++ b/R/preprocessDb.R
@@ -39,7 +39,7 @@
 
 preprocessDb<- function(x, genome=genome, qc=qc){
 
-  x <- as.matrix(x)
+#  x <- as.matrix(x)
   row.names(x)<- toupper(row.names(x))
 
   if (length(unique(colnames(x))) != ncol(x)){