From 0b74154137dc0f49ebece3185f611b1ba3176ea1 Mon Sep 17 00:00:00 2001
From: Tomrrr1 <76951517+Tomrrr1@users.noreply.github.com>
Date: Mon, 4 Mar 2024 14:42:15 +0000
Subject: [PATCH] Manual updates

---
 .DS_Store                        | Bin 10244 -> 10244 bytes
 .github/workflows/rworkflows.yml |   4 ++--
 DESCRIPTION                      |   2 +-
 NAMESPACE                        |   2 --
 README.md                        |  15 ++++++++-------
 man/conservative_idr.Rd          |   1 +
 man/multiple_replicates_mspc.Rd  |   3 +--
 man/optimal_idr.Rd               |   1 +
 man/pool_files.Rd                |  12 ++++++------
 man/prepare_named_list.Rd        |   1 +
 man/run_chipr.Rd                 |   2 +-
 11 files changed, 22 insertions(+), 21 deletions(-)

diff --git a/.DS_Store b/.DS_Store
index a106ae9cf656b85c27fcd0c8c5c1b4322fcc7382..cd90ad7d58c577a745fc2beddc156128369fdb20 100644
GIT binary patch
delta 97
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delta 868
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H=<$35BH+wJ

diff --git a/.github/workflows/rworkflows.yml b/.github/workflows/rworkflows.yml
index f953821..37ddb22 100644
--- a/.github/workflows/rworkflows.yml
+++ b/.github/workflows/rworkflows.yml
@@ -21,7 +21,7 @@ jobs:
       fail-fast: ${{ false }}
       matrix:
         config:
-        - os: ubuntu-latest
+        - os: ubuntu-latest # not run on Windows because MACSr is not supported.
           bioc: devel
           r: auto
           cont: ghcr.io/bioconductor/bioconductor_docker:devel
@@ -44,7 +44,7 @@ jobs:
         auto-activate-base: false
     - uses: neurogenomics/rworkflows@master
       with:
-        run_bioccheck: ${{ true }}
+        run_bioccheck: ${{ false }}
         run_rcmdcheck: ${{ true }}
         as_cran: ${{ true }}
         run_vignettes: ${{ true }}
diff --git a/DESCRIPTION b/DESCRIPTION
index 1b31a86..7fcf7fa 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -38,4 +38,4 @@ Config/testthat/edition: 3
 RoxygenNote: 7.3.1
 BugReports: https://github.com/neurogenomics/ConsensusPeak/issues
 VignetteBuilder: knitr
-biocViews: Epigenetics, PeakDetection, EpigeneticsWorkflow, ChIPSeq
+biocViews: Epigenetics, PeakDetection, ChIPSeq
diff --git a/NAMESPACE b/NAMESPACE
index fe7fb75..18cd0db 100644
--- a/NAMESPACE
+++ b/NAMESPACE
@@ -1,14 +1,12 @@
 # Generated by roxygen2: do not edit by hand
 
 export(calculate_idr)
-export(conservative_idr)
 export(feature_counts_matrix)
 export(generate_pseudoreplicates)
 export(idr_analysis)
 export(macs_call_peak)
 export(multiple_replicates_chipr)
 export(multiple_replicates_mspc)
-export(optimal_idr)
 import(ChIPpeakAnno)
 import(GenomicAlignments)
 import(GenomicRanges)
diff --git a/README.md b/README.md
index 0ae8cb4..e41c866 100644
--- a/README.md
+++ b/README.md
@@ -42,13 +42,14 @@ rep_treat_2 <- system.file("extdata",
 Run MACS3 peak calling and IDR thresholding with a single command:
 
 ```R
-result <- conservative_idr(
-  treat_files = c(rep_treat_1, rep_treat_2),
-  out_dir = ".", # Directory to write the output files
-  idr_stringent = TRUE, # Threshold at 0.01 or 0.05
-  is_paired = FALSE, # Is the data paired-end?
-  nomodel = TRUE # MACS3 setting
-  )
+result <- idr_analysis(treat_files = c(rep_treat_1, rep_treat_2),
+                       control_files = NULL,
+                       type = "conservative",
+                       is_paired = FALSE, # Is the data paired-end?
+                       idr_stringent = TRUE # Threshold at 0.01 or 0.05
+                       out_dir = ".", # Directory to write the output files
+                       nomodel = TRUE # MACS3 setting
+                       )
 ```
 
 
diff --git a/man/conservative_idr.Rd b/man/conservative_idr.Rd
index d6c508e..1a30d29 100644
--- a/man/conservative_idr.Rd
+++ b/man/conservative_idr.Rd
@@ -110,3 +110,4 @@ to the output files.
 \code{conservative_idr()} performs the conservative IDR analysis as defined
 by ENCODE. The function writes a filtered set of peaks to a desired location.
 }
+\keyword{internal}
diff --git a/man/multiple_replicates_mspc.Rd b/man/multiple_replicates_mspc.Rd
index df06a22..58d4a98 100644
--- a/man/multiple_replicates_mspc.Rd
+++ b/man/multiple_replicates_mspc.Rd
@@ -2,8 +2,7 @@
 % Please edit documentation in R/multiple_replicates_mspc.R
 \name{multiple_replicates_mspc}
 \alias{multiple_replicates_mspc}
-\title{Call peaks with MACSr and generate a consensus set with Multiple Sample Peak
-Calling (MSPC)}
+\title{Multiple replicate peak calling with MSPC}
 \usage{
 multiple_replicates_mspc(
   treat_files,
diff --git a/man/optimal_idr.Rd b/man/optimal_idr.Rd
index 8ae88fd..a3b263d 100644
--- a/man/optimal_idr.Rd
+++ b/man/optimal_idr.Rd
@@ -110,3 +110,4 @@ Summary of the IDR output
 biological replicate BAM files, shuffling reads, splitting into
 pseudoreplicates and calling peaks on the pseudoreplicates.
 }
+\keyword{internal}
diff --git a/man/pool_files.Rd b/man/pool_files.Rd
index e6f25ac..2185231 100644
--- a/man/pool_files.Rd
+++ b/man/pool_files.Rd
@@ -9,13 +9,12 @@ pool_files(named_list, out_dir)
 \arguments{
 \item{named_list}{A named list containing paths to BAM files.
 This list is outputted from the `prepare_named_list` function.
+
 The list includes:
-\itemize{
-  \item{"treatment_file_1"}{Path to the first treatment replicate.}
-  \item{"treatment_file_2"}{Path to the second treatment replicate.}
-  \item{"control_file_1"}{Optional. Path to the first control replicate.}
-  \item{"control_file_2"}{Optional. Path to the second control replicate.}
-}}
+- "treatment_file_1" Path to the first treatment replicate.
+- "treatment_file_2" Path to the second treatment replicate.
+- "control_file_1" Optional. Path to the first control replicate.
+- "control_file_2" Optional. Path to the second control replicate.}
 
 \item{out_dir}{The directory where the merged BAM files will be saved.}
 }
@@ -28,3 +27,4 @@ designed to work with the output from the `prepare_named_list` function,
 which provides a named list of BAM file paths. If control files are provided,
 they are also merged into a separate control BAM file.
 }
+\keyword{internal}
diff --git a/man/prepare_named_list.Rd b/man/prepare_named_list.Rd
index 3b19c6c..36dd08d 100644
--- a/man/prepare_named_list.Rd
+++ b/man/prepare_named_list.Rd
@@ -23,3 +23,4 @@ This function checks the validity of user-specified file paths for replicates
 and controls and constructs a named list. The function ensures that the file
 paths are valid and normalises them.
 }
+\keyword{internal}
diff --git a/man/run_chipr.Rd b/man/run_chipr.Rd
index 4a9e912..1748ce7 100644
--- a/man/run_chipr.Rd
+++ b/man/run_chipr.Rd
@@ -2,7 +2,7 @@
 % Please edit documentation in R/run_chipr.R
 \name{run_chipr}
 \alias{run_chipr}
-\title{Call consensus peaks using ChIP-R}
+\title{Multiple replicates peak calling with ChIP-R}
 \usage{
 run_chipr(
   peak_files,