pr comments: improve documentation

R/bins_to_bedgraph.R

@@ -6,7 +6,7 @@
 #' @param min_value Minimum value to retain the bin.
 #' @param filename Path to a local file on drive to save the resulting file.
 #'
-#' @return file
+#' @return full path to the file that was written
 #'
 #' @export
 bins_to_bedgraph = function(bin_df,min_value = 3,filename = "test.bed"){
@@ -17,8 +17,8 @@ bins_to_bedgraph = function(bin_df,min_value = 3,filename = "test.bed"){
     bed_cols = mutate(bed_cols,chr = paste0("chr",chr))
   }
   bed_cols = dplyr::filter(bed_cols,value > min_value)
-  this = dplyr::filter(chr1p,bin_start==27985000) 
+  this = dplyr::filter(chr1p,bin_start==27985000)
   bed_cols = mutate(bed_cols,end=format(end, scientific=F),start=format(start, scientific=F))
   write.table(bed_cols,row.names=F,col.names=F,quote=F,sep="\t",file=filename)
-
+  return(filename)
 }

R/cache_output.R

@@ -9,7 +9,7 @@
 #' @param function_params TODO.
 #' @param additional_details TODO.
 #'
-#' @return file
+#' @return full path to the file that was written
 #'
 #' @export
 cache_output = function(result_df,
@@ -44,4 +44,5 @@ cache_output = function(result_df,
 
   message(paste("creating/overwriting",cache_file_name))
   write_tsv(result_df,file=cache_file_name)
+  return(cache_file_name)
 }

R/calculate_tmb.R

@@ -1,4 +1,4 @@
-#' @title Return TMB counts.
+#' @title Calculate tumour mutation burden.
 #'
 #' @description This function implements tumor mutation burden calculation.
 #' TODO: add more details.

R/copy_no_clobber.R

@@ -6,7 +6,7 @@
 #' @param to_file TODO.
 #' @param force TODO.
 #'
-#' @return file
+#' @return full path to the file that was written
 #'
 #' @export
 copy_no_clobber = function(from_file,
@@ -19,4 +19,5 @@ copy_no_clobber = function(from_file,
   if(force){
     file.copy(from_file,to_file)
   }
+  return(to_file)
 }