@@ -105,12 +105,22 @@ getValueOrRds <- function(input)

 #' @importFrom tools file_ext

 nrowHelper <- function(data)

 {

+    nrowMtx <- function(file)

+    {

+        i <- 1

+        while (unname(data.table::fread(file, nrows=i, fill=TRUE)[i,1] == "%"))

+        {

+            i <- i + 1

+        }

+        return(unname(as.numeric(data.table::fread(file, nrow=i, fill=TRUE)[i,1])))

+    }

+

     if (is(data, "character"))

     {

         return(switch(tools::file_ext(data),

             "csv" = nrow(data.table::fread(data, select=1)),

             "tsv" = nrow(data.table::fread(data, select=1)),

-            "mtx" = as.numeric(data.table::fread(data, nrows=1, fill=TRUE)[1,1]),

+            "mtx" = nrowMtx(data),

             "gct" = as.numeric(strsplit(as.matrix(data.table::fread(data, nrows=1, sep='\t')), "\\s+")[[1]][1])

         ))

     }

@@ -126,12 +136,22 @@ nrowHelper <- function(data)

 #' @importFrom tools file_ext

 ncolHelper <- function(data)

 {

+    ncolMtx <- function(file)

+    {

+        i <- 1

+        while (unname(data.table::fread(file, nrows=i, fill=TRUE)[i,1] == "%"))

+        {

+            i <- i + 1

+        }

+        return(unname(as.numeric(data.table::fread(file, nrow=i, fill=TRUE)[i,2])))

+    }

+

     if (is(data, "character"))

     {

         return(switch(tools::file_ext(data),

             "csv" = ncol(data.table::fread(data, nrows=1)) - 1,

             "tsv" = ncol(data.table::fread(data, nrows=1)) - 1,

-            "mtx" = as.numeric(data.table::fread(data, nrows=1, fill=TRUE)[1,2]),

+            "mtx" = ncolMtx(data),

             "gct" = as.numeric(strsplit(as.matrix(data.table::fread(data, nrows=1, sep='\t')), "\\s+")[[1]][2])

         ))

     }

@@ -216,7 +216,7 @@ setGeneric("setParam", function(object, whichParam, value)

 #' @examples

 #'  params <- new("CogapsParams")

 #'  params <- setDistributedParams(params, 5)

-setGeneric("setDistributedParams", function(object, nSets, cut=NULL,

+setGeneric("setDistributedParams", function(object, nSets=NULL, cut=NULL,

 minNS=NULL, maxNS=NULL)

     {standardGeneric("setDistributedParams")})