From 8839fc1227b9054c0a22b387d07f2ce61cfe7346 Mon Sep 17 00:00:00 2001
From: Kdreval <k.dreval@gmail.com>
Date: Fri, 15 Mar 2024 09:34:34 -0700
Subject: [PATCH] pr comments: improve documentation

---
 R/bins_to_bedgraph.R    | 6 +++---
 R/cache_output.R        | 3 ++-
 R/calculate_tmb.R       | 2 +-
 R/copy_no_clobber.R     | 3 ++-
 man/bins_to_bedgraph.Rd | 2 +-
 man/cache_output.Rd     | 2 +-
 man/calculate_tmb.Rd    | 2 +-
 man/copy_no_clobber.Rd  | 2 +-
 8 files changed, 12 insertions(+), 10 deletions(-)

diff --git a/R/bins_to_bedgraph.R b/R/bins_to_bedgraph.R
index 97ac777..7a520e3 100644
--- a/R/bins_to_bedgraph.R
+++ b/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)
 }
diff --git a/R/cache_output.R b/R/cache_output.R
index 92b576e..64bc573 100644
--- a/R/cache_output.R
+++ b/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)
 }
diff --git a/R/calculate_tmb.R b/R/calculate_tmb.R
index 0d61faf..ebda2ed 100644
--- a/R/calculate_tmb.R
+++ b/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.
diff --git a/R/copy_no_clobber.R b/R/copy_no_clobber.R
index e15e43b..8750b83 100644
--- a/R/copy_no_clobber.R
+++ b/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)
 }
diff --git a/man/bins_to_bedgraph.Rd b/man/bins_to_bedgraph.Rd
index 5a94d39..97c05ce 100644
--- a/man/bins_to_bedgraph.Rd
+++ b/man/bins_to_bedgraph.Rd
@@ -14,7 +14,7 @@ bins_to_bedgraph(bin_df, min_value = 3, filename = "test.bed")
 \item{filename}{Path to a local file on drive to save the resulting file.}
 }
 \value{
-file
+full path to the file that was written
 }
 \description{
 This function will generate bed file.
diff --git a/man/cache_output.Rd b/man/cache_output.Rd
index 5176b2c..c772f23 100644
--- a/man/cache_output.Rd
+++ b/man/cache_output.Rd
@@ -28,7 +28,7 @@ cache_output(
 \item{additional_details}{TODO.}
 }
 \value{
-file
+full path to the file that was written
 }
 \description{
 TODO.
diff --git a/man/calculate_tmb.Rd b/man/calculate_tmb.Rd
index 77f6563..9dca146 100644
--- a/man/calculate_tmb.Rd
+++ b/man/calculate_tmb.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/calculate_tmb.R
 \name{calculate_tmb}
 \alias{calculate_tmb}
-\title{Return TMB counts.}
+\title{Calculate tumour mutation burden.}
 \usage{
 calculate_tmb(
   maf_data,
diff --git a/man/copy_no_clobber.Rd b/man/copy_no_clobber.Rd
index 1f3132a..af22267 100644
--- a/man/copy_no_clobber.Rd
+++ b/man/copy_no_clobber.Rd
@@ -14,7 +14,7 @@ copy_no_clobber(from_file, to_file, force = FALSE)
 \item{force}{TODO.}
 }
 \value{
-file
+full path to the file that was written
 }
 \description{
 TODO.