Add installation instructions to README. Edit function documentation.

R/conservative_idr.R

@@ -21,7 +21,7 @@
 #' @returns A list containing a summary of the IDR analysis along with the path
 #' to the output files.
 #'
-#' @export
+#' @keywords internal
 
 conservative_idr <- function(treat_files,
                              control_files = NULL,

R/feature_counts_matrix.R

@@ -22,7 +22,7 @@ feature_counts_matrix <- function(peak_file,
   # Read the peak file and subset desired columns
   peak <-
     utils::read.table(peak_file, header = FALSE)
-  peak_df <- peak[, c(4, 1, 2, 3, 6)]
+  peak_df <- peak[, c(4, 1, 2, 3, 6)] # name, chr, start, end, strand
 
   # Set column names for SAF format
   colnames(peak_df) <- c("GeneID", "Chr", "Start", "End", "Strand")

R/optimal_idr.R

@@ -10,7 +10,7 @@
 #'
 #' @returns Summary of the IDR output
 #'
-#' @export
+#' @keywords internal
 optimal_idr <- function(treat_files,
                         control_files = NULL,
                         is_paired,

R/pool_files.R

@@ -7,17 +7,19 @@
 #'
 #' @param 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.
+#'
 #' @param out_dir The directory where the merged BAM files will be saved.
 #' @return Vector containing file paths to the output BAM files
+#'
+#' @keywords internal
 
-pool_files <- function(named_list,
+pool_files <- function(named_list, # formatted by prepare_named_list
                        out_dir) {
   rep1 <- named_list[["treatment_file_1"]]
   rep2 <- named_list[["treatment_file_2"]]

R/prepare_named_list.R

@@ -11,6 +11,8 @@
 #' "treatment_file_2", "control_file_1", and "control_file_2", corresponding
 #' to the provided file paths. The list is filtered to exclude any that are
 #' NULL.
+#'
+#' @keywords internal
 
 prepare_named_list <- function(treat_files,
                                control_files = NULL) {

R/process_peak_file.R

@@ -10,7 +10,7 @@ process_peak_file <- function(peak_list,
   for (i in seq_along(peak_files)) {
     peak_file <- peak_files[i]
     peak <- utils::read.table(peak_file, header = FALSE)
-    peak_df <- peak[, c(1, 2, 3, 4, 8, 6)] # macs3 columns required for MSPC
+    peak_df <- peak[, c(1, 2, 3, 4, 8, 6)] # MACS3 columns required for MSPC
 
     output_file_path <- file.path(out_dir,
                                   paste0("processed_peak_rep_", i, ".bed"))

README.md

@@ -13,9 +13,60 @@ Authors: <i>Thomas Roberts</i>
 </h4>
 2024-02-04
 
-## R Markdown
+## Introduction
 
-Package for calling consensus peaks from multiple biological replicates. 
+`ConsensusPeak` is an R Package for calling consensus peaks from multiple 
+biological replicates. We implement several methods for thresholding, including 
+IDR conservative, IDR optimal, MSPC and ChIP-R.
 
-The package is unsupported on Windows because of its use of MACSr, a 
-bioconductor package that is itself unsupported.
+## Installation
+
+```R
+if(!require("remotes")) install.packages("remotes")
+remotes::install_github("neurogenomics/ConsensusPeak")
+```
+
+## Usage
+
+Load example data:
+
+```R
+rep_treat_1 <- system.file("extdata",
+                           "r1_creb_chr22.bam",
+                           package = "ConsensusPeak")
+rep_treat_2 <- system.file("extdata",
+                           "r2_creb_chr22.bam",
+                           package = "ConsensusPeak")
+```
+
+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
+  )
+```
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