added vararg to meshclustR

R/meshclustR.R

@@ -17,6 +17,7 @@
 #' Numeric values will be used as clustering thresholds for meshclust to override
 #' the automatically set threshold. If FALSE, meshclust will determine the
 #' threshold (recommended).
+#' @param ... pass on any additional strings to the meshclust commandline tool.
 #' @return A data frame with information regarding the clustering analysis.
 #'
 #' @examples
@@ -28,7 +29,8 @@
 meshclustR <- function(seqs = MyDNAStringSet,
                        meshclust_bin = meshclust,
                        filepath = path,
-                       threshold = FALSE){
+                       threshold = FALSE,
+                       ...){
 
   #create temporary file path
   temp_file <- file.path(filepath, 'cluster_me.fa')
@@ -42,10 +44,12 @@ meshclustR <- function(seqs = MyDNAStringSet,
   if(is.numeric(threshold) && 0 < threshold && threshold <= 0.99){
     system2(meshclust, args = c("-d", temp_file,
                                 "-o", out_file,
-                                "-t", threshold))
+                                "-t", threshold,
+                                ...))
   }else{
     system2(meshclust, args = c("-d", temp_file,
-                                "-o", out_file))
+                                "-o", out_file,
+                                ...))
   }
 
   #read output file and parse

man/meshclustR.Rd

@@ -8,7 +8,8 @@ meshclustR(
   seqs = MyDNAStringSet,
   meshclust_bin = meshclust,
   filepath = path,
-  threshold = FALSE
+  threshold = FALSE,
+  ...
 )
 }
 \arguments{
@@ -24,6 +25,8 @@ files will be saved.}
 Numeric values will be used as clustering thresholds for meshclust to override
 the automatically set threshold. If FALSE, meshclust will determine the
 threshold (recommended).}
+
+\item{...}{pass on any additional strings to the meshclust commandline tool.}
 }
 \value{
 A data frame with information regarding the clustering analysis.