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neurogenomics · Mar 4, 2024 · 0b74154 · 0b74154
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commit 0b74154
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Showing 11 changed files with 22 additions and 21 deletions.
diff --git a/.DS_Store b/.DS_Store
diff --git 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
@@ -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
@@ -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
@@ -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
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/man/pool_files.Rd b/man/pool_files.Rd
diff --git a/man/prepare_named_list.Rd b/man/prepare_named_list.Rd
diff --git a/man/run_chipr.Rd b/man/run_chipr.Rd