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neurogenomics · Mar 4, 2024 · e12a4d3 · e12a4d3
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diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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
diff --git a/man/multiple_replicates_chipr.Rd b/man/multiple_replicates_chipr.Rd
diff --git a/man/multiple_replicates_mspc.Rd b/man/multiple_replicates_mspc.Rd
diff --git a/man/optimal_idr.Rd b/man/optimal_idr.Rd
diff --git 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
                          )