diff --git a/R/FEAST.R b/R/FEAST.R
index 149be09..1782291 100644
--- a/R/FEAST.R
+++ b/R/FEAST.R
@@ -41,8 +41,7 @@
 #' }
 #'
 #' @export
-FEAST <- function(C, metadata, EM_iterations = 1000, COVERAGE = NULL ,different_sources_flag,
-                  dir_path, outfile){
+FEAST <- function(C, metadata, EM_iterations = 1000, COVERAGE = NULL ,different_sources_flag, dir_path = NULL, outfile = NULL){
 
   ###1. Parse metadata and check it has the correct hearer (i.e., Env, SourceSink,	id)
   if(sum(colnames(metadata)=='Env')==0) stop("The metadata file must contain an 'Env' column naming the source environment for each sample.")
@@ -143,9 +142,11 @@ FEAST <- function(C, metadata, EM_iterations = 1000, COVERAGE = NULL ,different_
   colnames(proportions_mat) <- c(envs_sources, "Unknown")
   rownames(proportions_mat) <- envs_sink
   # proportions_mat[is.na(proportions_mat)] <- 999
+  if(!is.null(dir_path)){
+    setwd(dir_path)
+    write.table(proportions_mat, file = paste0(outfile,"_source_contributions_matrix.txt"), sep = "\t")
+  }
 
-  setwd(dir_path)
-  write.table(proportions_mat, file = paste0(outfile,"_source_contributions_matrix.txt"), sep = "\t")
   return(proportions_mat)
 
 }
diff --git a/R/Infer_LatentVariables.R b/R/Infer_LatentVariables.R
index 82943c7..30f3001 100644
--- a/R/Infer_LatentVariables.R
+++ b/R/Infer_LatentVariables.R
@@ -129,7 +129,6 @@ unknown_initialize_1 <- function(sources, sink, n_sources){
   sources_sum <- apply(sources, 2 ,sum)
 
 
-  unknown_source <- c()
 
   if(n_sources > 1){
 
@@ -169,7 +168,7 @@ unknown_initialize_1 <- function(sources, sink, n_sources){
     if(length(ind_cor_all) > 1){
 
       cor_abundance <- round(apply(sources[,ind_cor_all], 2, min)/2) #take the min abundnace of the 'cor'
-      unknown_source[ind_cor_all] <- 0
+      unknown_source[ind_cor_all] <- cor_abundance
 
 
     }
diff --git a/R/utils.R b/R/utils.R
index d346034..1228cfc 100644
--- a/R/utils.R
+++ b/R/utils.R
@@ -44,7 +44,7 @@ FEAST_rarefy <- function(x,maxdepth){
 
   if(is.null(maxdepth)) return(x)
 
-  if(!is.element(class(x), c('matrix', 'data.frame','array')))
+  if(!any(is.element(class(x), c('matrix', 'data.frame','array'))))
     x <- matrix(x,nrow=nrow(x))
   nr <- nrow(x)
   nc <- ncol(x)