From 0cd61935a8f3836f2f9dd8eb57c7c5cb35b6cabd Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 13 Feb 2026 17:29:58 +0000
Subject: [PATCH 1/5] Initial plan


From a8807397f3789f676cd09fe4400c29b2b6a5e4eb Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 13 Feb 2026 17:36:37 +0000
Subject: [PATCH 2/5] Update multiomics function documentation and run
 devtools::document()

Co-authored-by: MVesuviusC <5831817+MVesuviusC@users.noreply.github.com>
---
 DESCRIPTION                  |   2 +-
 R/multiomics.R               | 210 +++++++++++++++++++++++++----------
 man/add_nucleosome_signal.Rd |  17 ++-
 man/annotate_atac.Rd         |  20 +++-
 man/calc_frip.Rd             |  29 +++--
 man/merge_atac.Rd            |  35 ++++--
 man/merge_gex_atac.Rd        |  35 ++++--
 man/process_seurat.Rd        |  11 --
 man/process_seurat_atac.Rd   |  32 ++++--
 man/r_dim_plot.Rd            |   6 -
 man/r_feature_plot.Rd        |  16 ---
 man/tss_enrichment.Rd        |  17 ++-
 12 files changed, 286 insertions(+), 144 deletions(-)

diff --git a/DESCRIPTION b/DESCRIPTION
index 4dbac79..ef576e0 100644
--- a/DESCRIPTION
+++ b/DESCRIPTION
@@ -10,7 +10,7 @@ Description: This is a set of utility functions designed for single cell
 License: MIT + file LICENSE
 Encoding: UTF-8
 LazyData: true
-RoxygenNote: 7.2.3
+RoxygenNote: 7.3.1
 Imports:
     magrittr,
     ggplot2,
diff --git a/R/multiomics.R b/R/multiomics.R
index d332bed..835dd94 100644
--- a/R/multiomics.R
+++ b/R/multiomics.R
@@ -1,20 +1,35 @@
 #' Merge multiple ATAC-seq samples into a single Seurat object
 #'
-#' FUNCTION_DESCRIPTION
-#'
-#' @param peak_beds DESCRIPTION.
-#' @param min_peak_width DESCRIPTION.
-#' @param max_peak_width DESCRIPTION.
-#' @param frag_paths DESCRIPTION.
-#' @param cell_ids DESCRIPTION.
-#' @param n_regions_simul DESCRIPTION.
-#' @param threads Number of threads to use.
+#' Reads peak BED files, reduces overlapping peaks, and creates a merged
+#' Seurat object with ATAC-seq data from multiple samples.
+#'
+#' @param peak_beds Character vector of paths to BED files containing peak
+#'     regions for each sample.
+#' @param min_peak_width Minimum width (in base pairs) for peaks to be
+#'     included in the analysis. Default is 20.
+#' @param max_peak_width Maximum width (in base pairs) for peaks to be
+#'     included in the analysis. Default is 10000.
+#' @param frag_paths Character vector of paths to fragment files (one per
+#'     sample).
+#' @param cell_ids Character vector of sample identifiers to prepend to cell
+#'     barcodes. Must be in the same order as frag_paths.
+#' @param n_regions_simul Number of regions to process simultaneously when
+#'     building the feature matrix. Default is 2000.
+#' @param threads Number of threads to use for parallel processing. Default
+#'     is 1.
 #'
 #' @export
 #'
-#' @return RETURN_DESCRIPTION
+#' @return A Seurat object with a merged ATAC assay containing data from all
+#'     samples.
 #' @examples
-#' # ADD_EXAMPLES_HERE
+#' \dontrun{
+#' merged_obj <- merge_atac(
+#'   peak_beds = c("sample1_peaks.bed", "sample2_peaks.bed"),
+#'   frag_paths = c("sample1_fragments.tsv.gz", "sample2_fragments.tsv.gz"),
+#'   cell_ids = c("sample1", "sample2")
+#' )
+#' }
 merge_atac <- function(peak_beds,
                        min_peak_width = 20,
                        max_peak_width = 10000,
@@ -72,16 +87,26 @@ merge_atac <- function(peak_beds,
 
 #' Add annotation to ATAC data in a Seurat object
 #'
-#' FUNCTION_DESCRIPTION
+#' Creates genomic annotations from a GTF file and adds them to the ATAC
+#' assay in a Seurat object. The function extracts transcript information,
+#' gene biotypes, and gene identifiers from the GTF file.
 #'
-#' @param sobject Seurat object to be processed
-#' @param gtf String of path to a gtf file.
+#' @param sobject Seurat object containing ATAC data to be annotated. The
+#'     default assay should be set to "ATAC" or "peaks" before calling this
+#'     function.
+#' @param gtf Character string specifying the path to a GTF file containing
+#'     genomic annotations.
 #'
 #' @export
 #'
-#' @return RETURN_DESCRIPTION
+#' @return A Seurat object with genomic annotations added to the ATAC assay.
 #' @examples
-#' # ADD_EXAMPLES_HERE
+#' \dontrun{
+#' atac_obj <- annotate_atac(
+#'   sobject = atac_seurat,
+#'   gtf = "path/to/genes.gtf"
+#' )
+#' }
 annotate_atac <- function(sobject,
                           gtf) {
     if (is.null(gtf)) {
@@ -135,16 +160,23 @@ annotate_atac <- function(sobject,
 
 #' Add nucleosome signal to ATAC data in a Seurat object
 #'
-#' FUNCTION_DESCRIPTION
+#' Calculates nucleosome signal for each cell using Signac and adds it as
+#' metadata. Also creates a categorical grouping variable based on the
+#' specified cutoff.
 #'
-#' @param sobject Seurat object to be processed
-#' @param cutoff DESCRIPTION.
+#' @param sobject Seurat object containing ATAC data to be processed.
+#' @param cutoff Numeric value for the nucleosome signal cutoff. Cells with
+#'     nucleosome signal above this value are grouped as "NS > cutoff" and
+#'     cells below are grouped as "NS < cutoff". Default is 4.
 #'
 #' @export
 #'
-#' @return RETURN_DESCRIPTION
+#' @return A Seurat object with nucleosome signal added as metadata in the
+#'     nucleosome_signal and nucleosome_group columns.
 #' @examples
-#' # ADD_EXAMPLES_HERE
+#' \dontrun{
+#' atac_obj <- add_nucleosome_signal(sobject = atac_seurat, cutoff = 4)
+#' }
 add_nucleosome_signal <- function(sobject,
                                   cutoff = 4) {
     sobject <- Signac::NucleosomeSignal(sobject)
@@ -156,16 +188,23 @@ add_nucleosome_signal <- function(sobject,
 
 #' Calculate TSS enrichment for a Seurat object
 #'
-#' FUNCTION_DESCRIPTION
+#' Calculates transcription start site (TSS) enrichment scores for each cell
+#' using Signac. Also creates a categorical variable indicating high or low
+#' TSS enrichment based on the specified cutoff.
 #'
-#' @param sobject Seurat object to be processed
-#' @param cutoff DESCRIPTION.
+#' @param sobject Seurat object containing ATAC data to be processed.
+#' @param cutoff Numeric value for the TSS enrichment cutoff. Cells with TSS
+#'     enrichment above this value are classified as "High" and cells below
+#'     are classified as "Low". Default is 2.
 #'
 #' @export
 #'
-#' @return RETURN_DESCRIPTION
+#' @return A Seurat object with TSS enrichment added as metadata in the
+#'     TSS.enrichment and high_tss columns.
 #' @examples
-#' # ADD_EXAMPLES_HERE
+#' \dontrun{
+#' atac_obj <- tss_enrichment(sobject = atac_seurat, cutoff = 2)
+#' }
 tss_enrichment <- function(sobject,
                            cutoff = 2) {
     sobject <- Signac::TSSEnrichment(sobject, fast = FALSE)
@@ -177,18 +216,33 @@ tss_enrichment <- function(sobject,
 
 #' Calculate FRiP for a Seurat object
 #'
-#' FUNCTION_DESCRIPTION
+#' Calculates the fraction of reads in peaks (FRiP) metric for each cell in
+#' an ATAC-seq Seurat object. This function counts fragments from the
+#' provided fragment files and calculates quality metrics including total
+#' fragments, mononucleosomal fragments, nucleosome-free fragments, and FRiP.
 #'
-#' @param sobject Seurat object to be processed
-#' @param frag_files Named list of fragment files. The names should be the
-#'    string to be prepended to the cell barcodes.
-#' @param verbose Should functions be verbose?
+#' @param sobject Seurat object containing ATAC data to be processed.
+#' @param frag_files Named list of paths to fragment files. The names should
+#'     correspond to sample identifiers that will be prepended to cell
+#'     barcodes (with an underscore separator). If providing a single
+#'     unnamed fragment file, cell names must follow standard CellRanger
+#'     format (e.g., "ATGC-1").
+#' @param verbose Logical indicating whether functions should produce
+#'     detailed output messages. Default is FALSE.
 #'
 #' @export
 #'
-#' @return RETURN_DESCRIPTION
+#' @return A Seurat object with FRiP and fragment count metadata added. If
+#'     there is a mismatch between cells in the object and fragment files, a
+#'     data frame of fragment counts is returned instead for inspection.
 #' @examples
-#' # ADD_EXAMPLES_HERE
+#' \dontrun{
+#' atac_obj <- calc_frip(
+#'   sobject = atac_seurat,
+#'   frag_files = list(sample1 = "path/to/fragments1.tsv.gz",
+#'                     sample2 = "path/to/fragments2.tsv.gz")
+#' )
+#' }
 calc_frip <- function(sobject,
                       frag_files,
                       verbose = FALSE) {
@@ -284,20 +338,34 @@ add_atac_metadata <- function(sobject,
 
 #' Process a Seurat object with ATAC data
 #'
-#' FUNCTION_DESCRIPTION
-#'
-#' @param sobject Seurat object to be processed
-#' @param assay Assay that has the ATAC data
-#' @param verbose Should functions be verbose?
-#' @param umap_dims PCA dimensions to use for UMAP
-#' @param resolution Resolution to be used in FindClusters
-#' @param reduction What reduction to be used to generate umap
+#' Performs standard ATAC-seq processing workflow including TF-IDF
+#' normalization, feature selection, dimensionality reduction using singular
+#' value decomposition (SVD/LSI), clustering, and UMAP generation.
+#'
+#' @param sobject Seurat object containing ATAC data to be processed.
+#' @param assay Name of the assay containing the ATAC data. Default is
+#'     "ATAC".
+#' @param verbose Logical indicating whether processing functions should
+#'     produce detailed output messages. Default is FALSE.
+#' @param umap_dims Integer vector specifying which LSI dimensions to use
+#'     for UMAP calculation. Default is 2:30 (dimensions 2 through 30).
+#' @param resolution Numeric value for clustering resolution passed to
+#'     FindClusters. Higher values result in more clusters. Default is 0.3.
+#' @param reduction Character string specifying which dimensionality
+#'     reduction to use for clustering and UMAP. Default is "lsi".
 #'
 #' @export
 #'
-#' @return A processed Seurat object
+#' @return A processed Seurat object with LSI reduction, UMAP coordinates
+#'     (stored as "umap_atac"), and cluster assignments. The original active
+#'     assay is restored after processing.
 #' @examples
-#' # ADD_EXAMPLES_HERE
+#' \dontrun{
+#' processed_atac <- process_seurat_atac(
+#'   sobject = atac_seurat,
+#'   resolution = 0.5
+#' )
+#' }
 process_seurat_atac <- function(sobject,
                                 assay = "ATAC",
                                 verbose = FALSE,
@@ -313,7 +381,9 @@ process_seurat_atac <- function(sobject,
         Signac::FindTopFeatures(min.cutoff = "q0", verbose = verbose) %>%
         Signac::RunSVD(verbose = verbose) %>%
         Seurat::FindNeighbors(reduction = reduction, verbose = verbose) %>%
-        Seurat::FindClusters(algorithm = 3, verbose = verbose, resolution = resolution) %>%
+        Seurat::FindClusters(algorithm = 3,
+                             verbose = verbose,
+                             resolution = resolution) %>%
         Seurat::RunUMAP(reduction = reduction,
                         dims = umap_dims,
                         verbose = verbose,
@@ -342,26 +412,45 @@ process_seurat_atac <- function(sobject,
 
 #' Merge GEX and ATAC data
 #'
-#' FUNCTION_DESCRIPTION
-#'
-#' @param gex_sobj Seurat object with GEX data to be processed
-#' @param atac_sobj Seurat object with ATAC data to be processed
-#' @param atac_assay_name Name of the assay in atac_sobj that has the ATAC data
-#' @param gex_pca_dims GEX PCA dimensions to use for UMAP
-#' @param atac_pca_dims ATAC PCA dimensions to use for UMAP
-#' @param verbose Should functions be verbose?
+#' Combines gene expression (GEX) and ATAC-seq data from separate Seurat
+#' objects into a single multimodal object. Performs joint dimensionality
+#' reduction and clustering using weighted nearest neighbor (WNN) analysis.
+#'
+#' @param gex_sobj Seurat object containing gene expression data. Should
+#'     have PCA reduction already computed.
+#' @param atac_sobj Seurat object containing ATAC-seq data. Should have LSI
+#'     reduction already computed.
+#' @param atac_assay_name Character string specifying the name of the ATAC
+#'     assay in atac_sobj. Default is "ATAC".
+#' @param gex_pca_dims Integer vector specifying which PCA dimensions to use
+#'     from the GEX data. Default uses all available PCA dimensions.
+#' @param atac_pca_dims Integer vector specifying which LSI dimensions to
+#'     use from the ATAC data. Default uses all available LSI dimensions.
+#' @param verbose Logical indicating whether processing functions should
+#'     produce detailed output messages. Default is FALSE.
 #'
 #' @export
 #'
-#' @return A processed Seurat object
+#' @return A Seurat object containing both RNA and ATAC assays with joint
+#'     UMAP coordinates and WNN-based cluster assignments. Only cells present
+#'     in both input objects are retained.
 #' @examples
-#' # ADD_EXAMPLES_HERE
+#' \dontrun{
+#' multimodal_obj <- merge_gex_atac(
+#'   gex_sobj = gex_seurat,
+#'   atac_sobj = atac_seurat,
+#'   gex_pca_dims = 1:30,
+#'   atac_pca_dims = 2:30
+#' )
+#' }
 merge_gex_atac <- function(gex_sobj,
                            atac_sobj,
                            atac_assay_name = "ATAC",
-                           gex_pca_dims = 1:dim(Seurat::Embeddings(gex_sobj))[2],
-                           atac_pca_dims = 1:dim(Seurat::Embeddings(atac_sobj,
-                                                                    reduction = "lsi"))[2],
+                           gex_pca_dims =
+                               1:dim(Seurat::Embeddings(gex_sobj))[2],
+                           atac_pca_dims =
+                               1:dim(Seurat::Embeddings(atac_sobj,
+                                                        reduction = "lsi"))[2],
                            verbose = FALSE) {
     # Make seurat object from GEX keeping only cells present in ATAC
     merged_data <-
@@ -385,9 +474,10 @@ merge_gex_atac <- function(gex_sobj,
     # Make joint UMAP
     merged_data <-
         merged_data %>%
-        Seurat::FindMultiModalNeighbors(reduction.list = list("pca", "lsi"),
-                                        dims.list = list(gex_pca_dims, atac_pca_dims),
-                                        verbose = verbose)
+        Seurat::FindMultiModalNeighbors(
+            reduction.list = list("pca", "lsi"),
+            dims.list = list(gex_pca_dims, atac_pca_dims),
+            verbose = verbose)
 
     # build a joint UMAP visualization
     merged_data <-
diff --git a/man/add_nucleosome_signal.Rd b/man/add_nucleosome_signal.Rd
index d8a0ddf..135f1a8 100644
--- a/man/add_nucleosome_signal.Rd
+++ b/man/add_nucleosome_signal.Rd
@@ -7,16 +7,23 @@
 add_nucleosome_signal(sobject, cutoff = 4)
 }
 \arguments{
-\item{sobject}{Seurat object to be processed}
+\item{sobject}{Seurat object containing ATAC data to be processed.}
 
-\item{cutoff}{DESCRIPTION.}
+\item{cutoff}{Numeric value for the nucleosome signal cutoff. Cells with
+nucleosome signal above this value are grouped as "NS > cutoff" and
+cells below are grouped as "NS < cutoff". Default is 4.}
 }
 \value{
-RETURN_DESCRIPTION
+A Seurat object with nucleosome signal added as metadata in the
+    nucleosome_signal and nucleosome_group columns.
 }
 \description{
-FUNCTION_DESCRIPTION
+Calculates nucleosome signal for each cell using Signac and adds it as
+metadata. Also creates a categorical grouping variable based on the
+specified cutoff.
 }
 \examples{
-# ADD_EXAMPLES_HERE
+\dontrun{
+atac_obj <- add_nucleosome_signal(sobject = atac_seurat, cutoff = 4)
+}
 }
diff --git a/man/annotate_atac.Rd b/man/annotate_atac.Rd
index 3a1fc29..361cc6f 100644
--- a/man/annotate_atac.Rd
+++ b/man/annotate_atac.Rd
@@ -7,16 +7,26 @@
 annotate_atac(sobject, gtf)
 }
 \arguments{
-\item{sobject}{Seurat object to be processed}
+\item{sobject}{Seurat object containing ATAC data to be annotated. The
+default assay should be set to "ATAC" or "peaks" before calling this
+function.}
 
-\item{gtf}{String of path to a gtf file.}
+\item{gtf}{Character string specifying the path to a GTF file containing
+genomic annotations.}
 }
 \value{
-RETURN_DESCRIPTION
+A Seurat object with genomic annotations added to the ATAC assay.
 }
 \description{
-FUNCTION_DESCRIPTION
+Creates genomic annotations from a GTF file and adds them to the ATAC
+assay in a Seurat object. The function extracts transcript information,
+gene biotypes, and gene identifiers from the GTF file.
 }
 \examples{
-# ADD_EXAMPLES_HERE
+\dontrun{
+atac_obj <- annotate_atac(
+  sobject = atac_seurat,
+  gtf = "path/to/genes.gtf"
+)
+}
 }
diff --git a/man/calc_frip.Rd b/man/calc_frip.Rd
index a349eeb..d489bff 100644
--- a/man/calc_frip.Rd
+++ b/man/calc_frip.Rd
@@ -7,19 +7,34 @@
 calc_frip(sobject, frag_files, verbose = FALSE)
 }
 \arguments{
-\item{sobject}{Seurat object to be processed}
+\item{sobject}{Seurat object containing ATAC data to be processed.}
 
-\item{frag_files}{Named list of fragment files. The names should be the
-string to be prepended to the cell barcodes.}
+\item{frag_files}{Named list of paths to fragment files. The names should
+correspond to sample identifiers that will be prepended to cell
+barcodes (with an underscore separator). If providing a single
+unnamed fragment file, cell names must follow standard CellRanger
+format (e.g., "ATGC-1").}
 
-\item{verbose}{Should functions be verbose?}
+\item{verbose}{Logical indicating whether functions should produce
+detailed output messages. Default is FALSE.}
 }
 \value{
-RETURN_DESCRIPTION
+A Seurat object with FRiP and fragment count metadata added. If
+    there is a mismatch between cells in the object and fragment files, a
+    data frame of fragment counts is returned instead for inspection.
 }
 \description{
-FUNCTION_DESCRIPTION
+Calculates the fraction of reads in peaks (FRiP) metric for each cell in
+an ATAC-seq Seurat object. This function counts fragments from the
+provided fragment files and calculates quality metrics including total
+fragments, mononucleosomal fragments, nucleosome-free fragments, and FRiP.
 }
 \examples{
-# ADD_EXAMPLES_HERE
+\dontrun{
+atac_obj <- calc_frip(
+  sobject = atac_seurat,
+  frag_files = list(sample1 = "path/to/fragments1.tsv.gz",
+                    sample2 = "path/to/fragments2.tsv.gz")
+)
+}
 }
diff --git a/man/merge_atac.Rd b/man/merge_atac.Rd
index b8b5cc0..a82fcf0 100644
--- a/man/merge_atac.Rd
+++ b/man/merge_atac.Rd
@@ -15,26 +15,41 @@ merge_atac(
 )
 }
 \arguments{
-\item{peak_beds}{DESCRIPTION.}
+\item{peak_beds}{Character vector of paths to BED files containing peak
+regions for each sample.}
 
-\item{min_peak_width}{DESCRIPTION.}
+\item{min_peak_width}{Minimum width (in base pairs) for peaks to be
+included in the analysis. Default is 20.}
 
-\item{max_peak_width}{DESCRIPTION.}
+\item{max_peak_width}{Maximum width (in base pairs) for peaks to be
+included in the analysis. Default is 10000.}
 
-\item{frag_paths}{DESCRIPTION.}
+\item{frag_paths}{Character vector of paths to fragment files (one per
+sample).}
 
-\item{cell_ids}{DESCRIPTION.}
+\item{cell_ids}{Character vector of sample identifiers to prepend to cell
+barcodes. Must be in the same order as frag_paths.}
 
-\item{n_regions_simul}{DESCRIPTION.}
+\item{n_regions_simul}{Number of regions to process simultaneously when
+building the feature matrix. Default is 2000.}
 
-\item{threads}{Number of threads to use.}
+\item{threads}{Number of threads to use for parallel processing. Default
+is 1.}
 }
 \value{
-RETURN_DESCRIPTION
+A Seurat object with a merged ATAC assay containing data from all
+    samples.
 }
 \description{
-FUNCTION_DESCRIPTION
+Reads peak BED files, reduces overlapping peaks, and creates a merged
+Seurat object with ATAC-seq data from multiple samples.
 }
 \examples{
-# ADD_EXAMPLES_HERE
+\dontrun{
+merged_obj <- merge_atac(
+  peak_beds = c("sample1_peaks.bed", "sample2_peaks.bed"),
+  frag_paths = c("sample1_fragments.tsv.gz", "sample2_fragments.tsv.gz"),
+  cell_ids = c("sample1", "sample2")
+)
+}
 }
diff --git a/man/merge_gex_atac.Rd b/man/merge_gex_atac.Rd
index 883f80a..ee1ef98 100644
--- a/man/merge_gex_atac.Rd
+++ b/man/merge_gex_atac.Rd
@@ -14,24 +14,41 @@ merge_gex_atac(
 )
 }
 \arguments{
-\item{gex_sobj}{Seurat object with GEX data to be processed}
+\item{gex_sobj}{Seurat object containing gene expression data. Should
+have PCA reduction already computed.}
 
-\item{atac_sobj}{Seurat object with ATAC data to be processed}
+\item{atac_sobj}{Seurat object containing ATAC-seq data. Should have LSI
+reduction already computed.}
 
-\item{atac_assay_name}{Name of the assay in atac_sobj that has the ATAC data}
+\item{atac_assay_name}{Character string specifying the name of the ATAC
+assay in atac_sobj. Default is "ATAC".}
 
-\item{gex_pca_dims}{GEX PCA dimensions to use for UMAP}
+\item{gex_pca_dims}{Integer vector specifying which PCA dimensions to use
+from the GEX data. Default uses all available PCA dimensions.}
 
-\item{atac_pca_dims}{ATAC PCA dimensions to use for UMAP}
+\item{atac_pca_dims}{Integer vector specifying which LSI dimensions to
+use from the ATAC data. Default uses all available LSI dimensions.}
 
-\item{verbose}{Should functions be verbose?}
+\item{verbose}{Logical indicating whether processing functions should
+produce detailed output messages. Default is FALSE.}
 }
 \value{
-A processed Seurat object
+A Seurat object containing both RNA and ATAC assays with joint
+    UMAP coordinates and WNN-based cluster assignments. Only cells present
+    in both input objects are retained.
 }
 \description{
-FUNCTION_DESCRIPTION
+Combines gene expression (GEX) and ATAC-seq data from separate Seurat
+objects into a single multimodal object. Performs joint dimensionality
+reduction and clustering using weighted nearest neighbor (WNN) analysis.
 }
 \examples{
-# ADD_EXAMPLES_HERE
+\dontrun{
+multimodal_obj <- merge_gex_atac(
+  gex_sobj = gex_seurat,
+  atac_sobj = atac_seurat,
+  gex_pca_dims = 1:30,
+  atac_pca_dims = 2:30
+)
+}
 }
diff --git a/man/process_seurat.Rd b/man/process_seurat.Rd
index 5bddb59..2b8c1cd 100644
--- a/man/process_seurat.Rd
+++ b/man/process_seurat.Rd
@@ -21,22 +21,11 @@ process_seurat(
 \arguments{
 \item{sobject}{A Seurat object}
 
-\item{verbose}{Controls verbosity}
-
 \item{pca_npcs}{Number of principal components to use in RunPCA(). Passed to npcs argument}
 
 \item{run_umap_dims}{Number of PCA dimensions to use in RunUMAP()
 and FindNeighbors()}
 
-\item{assay}{Assay to pull data for when using \code{features}, or assay used to construct Graph
-if running UMAP on a Graph}
-
-\item{resolution}{Value of the resolution parameter, use a value above
-(below) 1.0 if you want to obtain a larger (smaller) number of communities.}
-
-\item{reduction}{Which dimensional reduction (PCA or ICA) to use for the
-UMAP input. Default is PCA}
-
 \item{graph_name}{Name of graph to use for the clustering algorithm in FindClusters()}
 
 \item{neighbor_k_param}{Number of neighbors (k.param) to use in FindNeighbors()}
diff --git a/man/process_seurat_atac.Rd b/man/process_seurat_atac.Rd
index ec7e4d5..75fa86e 100644
--- a/man/process_seurat_atac.Rd
+++ b/man/process_seurat_atac.Rd
@@ -14,24 +14,38 @@ process_seurat_atac(
 )
 }
 \arguments{
-\item{sobject}{Seurat object to be processed}
+\item{sobject}{Seurat object containing ATAC data to be processed.}
 
-\item{assay}{Assay that has the ATAC data}
+\item{assay}{Name of the assay containing the ATAC data. Default is
+"ATAC".}
 
-\item{verbose}{Should functions be verbose?}
+\item{verbose}{Logical indicating whether processing functions should
+produce detailed output messages. Default is FALSE.}
 
-\item{umap_dims}{PCA dimensions to use for UMAP}
+\item{umap_dims}{Integer vector specifying which LSI dimensions to use
+for UMAP calculation. Default is 2:30 (dimensions 2 through 30).}
 
-\item{resolution}{Resolution to be used in FindClusters}
+\item{resolution}{Numeric value for clustering resolution passed to
+FindClusters. Higher values result in more clusters. Default is 0.3.}
 
-\item{reduction}{What reduction to be used to generate umap}
+\item{reduction}{Character string specifying which dimensionality
+reduction to use for clustering and UMAP. Default is "lsi".}
 }
 \value{
-A processed Seurat object
+A processed Seurat object with LSI reduction, UMAP coordinates
+    (stored as "umap_atac"), and cluster assignments. The original active
+    assay is restored after processing.
 }
 \description{
-FUNCTION_DESCRIPTION
+Performs standard ATAC-seq processing workflow including TF-IDF
+normalization, feature selection, dimensionality reduction using singular
+value decomposition (SVD/LSI), clustering, and UMAP generation.
 }
 \examples{
-# ADD_EXAMPLES_HERE
+\dontrun{
+processed_atac <- process_seurat_atac(
+  sobject = atac_seurat,
+  resolution = 0.5
+)
+}
 }
diff --git a/man/r_dim_plot.Rd b/man/r_dim_plot.Rd
index d930740..58be7d8 100644
--- a/man/r_dim_plot.Rd
+++ b/man/r_dim_plot.Rd
@@ -14,14 +14,8 @@ r_dim_plot(
 )
 }
 \arguments{
-\item{object}{Seurat object}
-
 \item{title}{Title to use for plot}
 
-\item{label}{Whether to label the clusters}
-
-\item{pt.size}{Adjust point size for plotting}
-
 \item{pt_alpha}{Transparency of points (should be between 0 and 1)}
 
 \item{...}{Other arguments to pass to Seurat::DimPlot}
diff --git a/man/r_feature_plot.Rd b/man/r_feature_plot.Rd
index d843b3d..7706fdf 100644
--- a/man/r_feature_plot.Rd
+++ b/man/r_feature_plot.Rd
@@ -7,24 +7,8 @@
 r_feature_plot(object, features, title = NULL, pt.size = 1, order = TRUE, ...)
 }
 \arguments{
-\item{object}{Seurat object}
-
-\item{features}{Vector of features to plot. Features can come from:
-\itemize{
-  \item An \code{Assay} feature (e.g. a gene name - "MS4A1")
-  \item A column name from meta.data (e.g. mitochondrial percentage -
-    "percent.mito")
-  \item A column name from a \code{DimReduc} object corresponding to the
-    cell embedding values (e.g. the PC 1 scores - "PC_1")
-}}
-
 \item{title}{Title to use for plot}
 
-\item{pt.size}{Adjust point size for plotting}
-
-\item{order}{Boolean determining whether to plot cells in order of expression. Can be useful if
-cells expressing given feature are getting buried.}
-
 \item{...}{Other arguments to pass to Seurat::FeaturePlot}
 }
 \value{
diff --git a/man/tss_enrichment.Rd b/man/tss_enrichment.Rd
index f19f809..c491a07 100644
--- a/man/tss_enrichment.Rd
+++ b/man/tss_enrichment.Rd
@@ -7,16 +7,23 @@
 tss_enrichment(sobject, cutoff = 2)
 }
 \arguments{
-\item{sobject}{Seurat object to be processed}
+\item{sobject}{Seurat object containing ATAC data to be processed.}
 
-\item{cutoff}{DESCRIPTION.}
+\item{cutoff}{Numeric value for the TSS enrichment cutoff. Cells with TSS
+enrichment above this value are classified as "High" and cells below
+are classified as "Low". Default is 2.}
 }
 \value{
-RETURN_DESCRIPTION
+A Seurat object with TSS enrichment added as metadata in the
+    TSS.enrichment and high_tss columns.
 }
 \description{
-FUNCTION_DESCRIPTION
+Calculates transcription start site (TSS) enrichment scores for each cell
+using Signac. Also creates a categorical variable indicating high or low
+TSS enrichment based on the specified cutoff.
 }
 \examples{
-# ADD_EXAMPLES_HERE
+\dontrun{
+atac_obj <- tss_enrichment(sobject = atac_seurat, cutoff = 2)
+}
 }

From 88c0a4184bb08ea5b0c9457c90525d305f070dea Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 13 Feb 2026 17:38:00 +0000
Subject: [PATCH 3/5] Revert unintended changes to non-multiomics documentation
 files

Co-authored-by: MVesuviusC <5831817+MVesuviusC@users.noreply.github.com>
---
 man/process_seurat.Rd | 11 +++++++++++
 man/r_dim_plot.Rd     |  6 ++++++
 man/r_feature_plot.Rd | 16 ++++++++++++++++
 3 files changed, 33 insertions(+)

diff --git a/man/process_seurat.Rd b/man/process_seurat.Rd
index 2b8c1cd..5bddb59 100644
--- a/man/process_seurat.Rd
+++ b/man/process_seurat.Rd
@@ -21,11 +21,22 @@ process_seurat(
 \arguments{
 \item{sobject}{A Seurat object}
 
+\item{verbose}{Controls verbosity}
+
 \item{pca_npcs}{Number of principal components to use in RunPCA(). Passed to npcs argument}
 
 \item{run_umap_dims}{Number of PCA dimensions to use in RunUMAP()
 and FindNeighbors()}
 
+\item{assay}{Assay to pull data for when using \code{features}, or assay used to construct Graph
+if running UMAP on a Graph}
+
+\item{resolution}{Value of the resolution parameter, use a value above
+(below) 1.0 if you want to obtain a larger (smaller) number of communities.}
+
+\item{reduction}{Which dimensional reduction (PCA or ICA) to use for the
+UMAP input. Default is PCA}
+
 \item{graph_name}{Name of graph to use for the clustering algorithm in FindClusters()}
 
 \item{neighbor_k_param}{Number of neighbors (k.param) to use in FindNeighbors()}
diff --git a/man/r_dim_plot.Rd b/man/r_dim_plot.Rd
index 58be7d8..d930740 100644
--- a/man/r_dim_plot.Rd
+++ b/man/r_dim_plot.Rd
@@ -14,8 +14,14 @@ r_dim_plot(
 )
 }
 \arguments{
+\item{object}{Seurat object}
+
 \item{title}{Title to use for plot}
 
+\item{label}{Whether to label the clusters}
+
+\item{pt.size}{Adjust point size for plotting}
+
 \item{pt_alpha}{Transparency of points (should be between 0 and 1)}
 
 \item{...}{Other arguments to pass to Seurat::DimPlot}
diff --git a/man/r_feature_plot.Rd b/man/r_feature_plot.Rd
index 7706fdf..d843b3d 100644
--- a/man/r_feature_plot.Rd
+++ b/man/r_feature_plot.Rd
@@ -7,8 +7,24 @@
 r_feature_plot(object, features, title = NULL, pt.size = 1, order = TRUE, ...)
 }
 \arguments{
+\item{object}{Seurat object}
+
+\item{features}{Vector of features to plot. Features can come from:
+\itemize{
+  \item An \code{Assay} feature (e.g. a gene name - "MS4A1")
+  \item A column name from meta.data (e.g. mitochondrial percentage -
+    "percent.mito")
+  \item A column name from a \code{DimReduc} object corresponding to the
+    cell embedding values (e.g. the PC 1 scores - "PC_1")
+}}
+
 \item{title}{Title to use for plot}
 
+\item{pt.size}{Adjust point size for plotting}
+
+\item{order}{Boolean determining whether to plot cells in order of expression. Can be useful if
+cells expressing given feature are getting buried.}
+
 \item{...}{Other arguments to pass to Seurat::FeaturePlot}
 }
 \value{

From a943d12b8bdfd6ec0bf10dd07214c13cd8fe8592 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 13 Feb 2026 17:59:17 +0000
Subject: [PATCH 4/5] Use @inheritParams to reduce duplication in multiomics
 documentation

Co-authored-by: MVesuviusC <5831817+MVesuviusC@users.noreply.github.com>
---
 R/multiomics.R           | 17 ++++++++---------
 man/add_atac_metadata.Rd | 16 ++++++++++++----
 2 files changed, 20 insertions(+), 13 deletions(-)

diff --git a/R/multiomics.R b/R/multiomics.R
index 835dd94..de21919 100644
--- a/R/multiomics.R
+++ b/R/multiomics.R
@@ -192,7 +192,7 @@ add_nucleosome_signal <- function(sobject,
 #' using Signac. Also creates a categorical variable indicating high or low
 #' TSS enrichment based on the specified cutoff.
 #'
-#' @param sobject Seurat object containing ATAC data to be processed.
+#' @inheritParams add_nucleosome_signal
 #' @param cutoff Numeric value for the TSS enrichment cutoff. Cells with TSS
 #'     enrichment above this value are classified as "High" and cells below
 #'     are classified as "Low". Default is 2.
@@ -221,7 +221,7 @@ tss_enrichment <- function(sobject,
 #' provided fragment files and calculates quality metrics including total
 #' fragments, mononucleosomal fragments, nucleosome-free fragments, and FRiP.
 #'
-#' @param sobject Seurat object containing ATAC data to be processed.
+#' @inheritParams add_nucleosome_signal
 #' @param frag_files Named list of paths to fragment files. The names should
 #'     correspond to sample identifiers that will be prepended to cell
 #'     barcodes (with an underscore separator). If providing a single
@@ -311,12 +311,12 @@ calc_frip <- function(sobject,
 #'
 #' Add nucleosome signal, TSS enrichment, and FRiP to a Seurat object
 #'
-#' @param sobject Seurat object to be processed
-#' @param gtf String of path to a gtf file.
+#' @inheritParams annotate_atac
+#' @inheritParams add_nucleosome_signal
+#' @inheritParams tss_enrichment
+#' @inheritParams calc_frip
 #' @param nucl_cutoff Cutoff for nucleosome signal
 #' @param tss_cutoff Cutoff for TSS enrichment
-#' @param frag_files Named list of paths to fragment files.
-#' @param verbose Should functions be verbose?
 #'
 #' @export
 #'
@@ -342,7 +342,7 @@ add_atac_metadata <- function(sobject,
 #' normalization, feature selection, dimensionality reduction using singular
 #' value decomposition (SVD/LSI), clustering, and UMAP generation.
 #'
-#' @param sobject Seurat object containing ATAC data to be processed.
+#' @inheritParams add_nucleosome_signal
 #' @param assay Name of the assay containing the ATAC data. Default is
 #'     "ATAC".
 #' @param verbose Logical indicating whether processing functions should
@@ -426,8 +426,7 @@ process_seurat_atac <- function(sobject,
 #'     from the GEX data. Default uses all available PCA dimensions.
 #' @param atac_pca_dims Integer vector specifying which LSI dimensions to
 #'     use from the ATAC data. Default uses all available LSI dimensions.
-#' @param verbose Logical indicating whether processing functions should
-#'     produce detailed output messages. Default is FALSE.
+#' @inheritParams process_seurat_atac
 #'
 #' @export
 #'
diff --git a/man/add_atac_metadata.Rd b/man/add_atac_metadata.Rd
index 52b7c87..4a479e2 100644
--- a/man/add_atac_metadata.Rd
+++ b/man/add_atac_metadata.Rd
@@ -14,17 +14,25 @@ add_atac_metadata(
 )
 }
 \arguments{
-\item{sobject}{Seurat object to be processed}
+\item{sobject}{Seurat object containing ATAC data to be annotated. The
+default assay should be set to "ATAC" or "peaks" before calling this
+function.}
 
-\item{gtf}{String of path to a gtf file.}
+\item{gtf}{Character string specifying the path to a GTF file containing
+genomic annotations.}
 
 \item{nucl_cutoff}{Cutoff for nucleosome signal}
 
 \item{tss_cutoff}{Cutoff for TSS enrichment}
 
-\item{frag_files}{Named list of paths to fragment files.}
+\item{frag_files}{Named list of paths to fragment files. The names should
+correspond to sample identifiers that will be prepended to cell
+barcodes (with an underscore separator). If providing a single
+unnamed fragment file, cell names must follow standard CellRanger
+format (e.g., "ATGC-1").}
 
-\item{verbose}{Should functions be verbose?}
+\item{verbose}{Logical indicating whether functions should produce
+detailed output messages. Default is FALSE.}
 }
 \value{
 A Seurat object

From 50bfc6f3f6e220821cb81abc927b7c5dfdfb9452 Mon Sep 17 00:00:00 2001
From: "copilot-swe-agent[bot]" <198982749+Copilot@users.noreply.github.com>
Date: Fri, 13 Feb 2026 18:00:29 +0000
Subject: [PATCH 5/5] Remove redundant @inheritParams directives

Co-authored-by: MVesuviusC <5831817+MVesuviusC@users.noreply.github.com>
---
 R/multiomics.R | 2 --
 1 file changed, 2 deletions(-)

diff --git a/R/multiomics.R b/R/multiomics.R
index de21919..2d981e7 100644
--- a/R/multiomics.R
+++ b/R/multiomics.R
@@ -312,8 +312,6 @@ calc_frip <- function(sobject,
 #' Add nucleosome signal, TSS enrichment, and FRiP to a Seurat object
 #'
 #' @inheritParams annotate_atac
-#' @inheritParams add_nucleosome_signal
-#' @inheritParams tss_enrichment
 #' @inheritParams calc_frip
 #' @param nucl_cutoff Cutoff for nucleosome signal
 #' @param tss_cutoff Cutoff for TSS enrichment