From e12a4d3e715599264a40ef0624f72e93bfeaec69 Mon Sep 17 00:00:00 2001
From: Tomrrr1 <76951517+Tomrrr1@users.noreply.github.com>
Date: Mon, 4 Mar 2024 15:59:40 +0000
Subject: [PATCH] Update documentation.

---
 DESCRIPTION                        | 2 +-
 R/conservative_idr.R               | 2 ++
 R/multiple_replicates_chipr.R      | 2 ++
 R/multiple_replicates_mspc.R       | 2 ++
 R/optimal_idr.R                    | 2 ++
 man/conservative_idr.Rd            | 3 +++
 man/multiple_replicates_chipr.Rd   | 3 +++
 man/multiple_replicates_mspc.Rd    | 3 +++
 man/optimal_idr.Rd                 | 3 +++
 tests/testthat/test-idr_analysis.R | 1 +
 10 files changed, 22 insertions(+), 1 deletion(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 7fcf7fa..d74db8a 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -1,6 +1,6 @@
 Package: ConsensusPeak
 Title: Call consensus peaks from multiple biological replicates
-Version: 0.0.0.9100
+Version: 0.0.0.9000
 Authors@R: 
   person(given = "Thomas", family = "Roberts", 
 	email = "tomroberts.work15@gmail.com", 
diff --git a/R/conservative_idr.R b/R/conservative_idr.R
index 2b7e969..ea0b953 100644
--- a/R/conservative_idr.R
+++ b/R/conservative_idr.R
@@ -4,6 +4,8 @@
 #' by ENCODE. The function writes a filtered set of peaks to a desired location.
 #'
 #' @inheritParams idr_analysis
+#' @param subdir_name Character specifying the name of the subdirectory that the
+#' output files will be placed.
 #' @inheritDotParams MACSr::callpeak -tfile -cfile -outdir -name -format -log
 #' -tempdir
 #'
diff --git a/R/multiple_replicates_chipr.R b/R/multiple_replicates_chipr.R
index b0e33b1..1041dad 100644
--- a/R/multiple_replicates_chipr.R
+++ b/R/multiple_replicates_chipr.R
@@ -4,6 +4,8 @@
 #' ChIP-R handles an arbitrary number of replicates.
 #'
 #' @inheritParams idr_analysis
+#' @param subdir_name Character specifying the name of the subdirectory that the
+#' output files will be placed.
 #' @inheritParams run_chipr
 #' @inheritDotParams MACSr::callpeak -tfile -cfile -outdir -name -format -log
 #' -tempdir
diff --git a/R/multiple_replicates_mspc.R b/R/multiple_replicates_mspc.R
index db07cc4..afab22b 100644
--- a/R/multiple_replicates_mspc.R
+++ b/R/multiple_replicates_mspc.R
@@ -5,6 +5,8 @@
 #' replicates.
 #'
 #' @inheritParams idr_analysis
+#' @param subdir_name Character specifying the name of the subdirectory that the
+#' output files will be placed.
 #' @inheritParams rmspc::mspc
 #' @inheritDotParams MACSr::callpeak -tfile -cfile -outdir -name -format -log
 #' -tempdir
diff --git a/R/optimal_idr.R b/R/optimal_idr.R
index f46f597..6a908af 100644
--- a/R/optimal_idr.R
+++ b/R/optimal_idr.R
@@ -5,6 +5,8 @@
 #' pseudoreplicates and calling peaks on the pseudoreplicates.
 #'
 #' @inheritParams idr_analysis
+#' @param subdir_name Character specifying the name of the subdirectory that the
+#' output files will be placed.
 #' @inheritDotParams MACSr::callpeak -tfile -cfile -outdir -name -format -log
 #' -tempdir
 #'
diff --git a/man/conservative_idr.Rd b/man/conservative_idr.Rd
index 43da68b..5e39479 100644
--- a/man/conservative_idr.Rd
+++ b/man/conservative_idr.Rd
@@ -37,6 +37,9 @@ ranges of the two replicates peaks. The default is `FALSE`.}
 will be created. By default, the results directories are created in
 tempdir().}
 
+\item{subdir_name}{Character specifying the name of the subdirectory that the
+output files will be placed.}
+
 \item{...}{
   Arguments passed on to \code{\link[MACSr:callpeak]{MACSr::callpeak}}
   \describe{
diff --git a/man/multiple_replicates_chipr.Rd b/man/multiple_replicates_chipr.Rd
index e307568..1106806 100644
--- a/man/multiple_replicates_chipr.Rd
+++ b/man/multiple_replicates_chipr.Rd
@@ -34,6 +34,9 @@ paired-end. The default is `FALSE`.}
 will be created. By default, the results directories are created in
 tempdir().}
 
+\item{subdir_name}{Character specifying the name of the subdirectory that the
+output files will be placed.}
+
 \item{minentries}{The minimum number of intersections a given peak must
 satisfy.}
 
diff --git a/man/multiple_replicates_mspc.Rd b/man/multiple_replicates_mspc.Rd
index 7d26422..1bf3546 100644
--- a/man/multiple_replicates_mspc.Rd
+++ b/man/multiple_replicates_mspc.Rd
@@ -34,6 +34,9 @@ paired-end. The default is `FALSE`.}
 will be created. By default, the results directories are created in
 tempdir().}
 
+\item{subdir_name}{Character specifying the name of the subdirectory that the
+output files will be placed.}
+
 \item{replicateType}{Character string. This argument defines
 the replicate type. Possible values of the argument : 
 'Bio','Biological', 'Tec', 'Technical'. 
diff --git a/man/optimal_idr.Rd b/man/optimal_idr.Rd
index d93da0a..1cf2c37 100644
--- a/man/optimal_idr.Rd
+++ b/man/optimal_idr.Rd
@@ -37,6 +37,9 @@ ranges of the two replicates peaks. The default is `FALSE`.}
 will be created. By default, the results directories are created in
 tempdir().}
 
+\item{subdir_name}{Character specifying the name of the subdirectory that the
+output files will be placed.}
+
 \item{...}{
   Arguments passed on to \code{\link[MACSr:callpeak]{MACSr::callpeak}}
   \describe{
diff --git a/tests/testthat/test-idr_analysis.R b/tests/testthat/test-idr_analysis.R
index 510b17a..7f62ce6 100644
--- a/tests/testthat/test-idr_analysis.R
+++ b/tests/testthat/test-idr_analysis.R
@@ -12,6 +12,7 @@ test_that("Optimal and conservative IDR peak files are generated", {
                          control_files = NULL,
                          type = "all",
                          is_paired = FALSE,
+                         keep_original = FALSE,
                          out_dir = temp_out_dir,
                          nomodel = TRUE
                          )