From 22bb41d19542d80e41319baffe06103289d1c437 Mon Sep 17 00:00:00 2001
From: James Eapen <james.eapen@vai.org>
Date: Wed, 3 Jul 2024 16:07:08 -0400
Subject: [PATCH] docs(threads): add query_all as OpenMP func; update nthread
 docs

---
 R/query_all.R      | 7 ++++---
 R/region_map.R     | 7 ++++---
 R/threads.R        | 3 ++-
 man/query_all.Rd   | 7 ++++---
 man/region_map.Rd  | 7 ++++---
 man/set_threads.Rd | 3 ++-
 6 files changed, 20 insertions(+), 14 deletions(-)

diff --git a/R/query_all.R b/R/query_all.R
index d809b2f..f57459f 100644
--- a/R/query_all.R
+++ b/R/query_all.R
@@ -1,11 +1,12 @@
 #' Make a bsseq object of CpGs from input genomic regions
 #'
 #' Queries the provided regions and produces M and Coverage matrices that are
-#' wrapped in a BSSeq object
+#' wrapped in a BSSeq object. Parallelized across files using threads from the
+#' `"iscream.threads"` option.
 #' @param bedfiles A vector of bedfile paths
 #' @param regions A vector of genomic regions strings
-#' @param nthreads Set number of threads to use. Should not be necessary as this
-#' is set by `option('iscream.threads')`
+#' @param nthreads Set number of threads to use overriding the
+#' `"iscream.threads"` option. See `?set_threads` for more information.
 #' @importFrom fs file_exists
 #' @return A data.frame
 #'
diff --git a/R/region_map.R b/R/region_map.R
index 91c1eda..238581d 100644
--- a/R/region_map.R
+++ b/R/region_map.R
@@ -1,15 +1,16 @@
 #' Run a defined function over genomic regions
 #'
 #' Run a function on the CpGs in bedfiles across genomic regions. Currently
-#' supported functions are aggregate and average.
+#' supported functions are aggregate and average. Parallelized across files
+#' using threads from the `"iscream.threads"` option.
 #' @param bedfiles A vector of bedfile paths
 #' @param regions A vector of genomic regions strings
 #' @param fun Function to apply over the region. See details.
 #' @param mval Whether to calculate the M value (coverage \eqn{\times \beta})
 #' or use the beta value
 #' when applying the function.
-#' @param nthreads Set number of threads to use. Should not be necessary as this
-#' is set by `option('iscream.threads')`
+#' @param nthreads Set number of threads to use overriding the
+#' `"iscream.threads"` option. See `?set_threads` for more information.
 #' @details
 #' Available functions:
 #' - `"aggregate"` sums the values in the region with aggregated beta values if
diff --git a/R/threads.R b/R/threads.R
index 50357aa..693afc1 100644
--- a/R/threads.R
+++ b/R/threads.R
@@ -56,10 +56,11 @@ get_threads <- function() {
 #' ```
 #' options(iscream.threads = [n_threads])
 #' ```
-#' in your .Rprofile. See help('Rprofile') for information on startup options.
+#' in your `.Rprofile` See `help('Rprofile')` for information on startup options.
 #'
 #' Functions currently using OpenMP:
 #' - `region_map()`
+#' - `query_all()`
 #'
 #' @export
 #'
diff --git a/man/query_all.Rd b/man/query_all.Rd
index a73069b..05f704b 100644
--- a/man/query_all.Rd
+++ b/man/query_all.Rd
@@ -11,15 +11,16 @@ query_all(bedfiles, regions, nthreads = NULL)
 
 \item{regions}{A vector of genomic regions strings}
 
-\item{nthreads}{Set number of threads to use. Should not be necessary as this
-is set by \code{option('iscream.threads')}}
+\item{nthreads}{Set number of threads to use overriding the
+\code{"iscream.threads"} option. See \code{?set_threads} for more information.}
 }
 \value{
 A data.frame
 }
 \description{
 Queries the provided regions and produces M and Coverage matrices that are
-wrapped in a BSSeq object
+wrapped in a BSSeq object. Parallelized across files using threads from the
+\code{"iscream.threads"} option.
 }
 \examples{
 bedfiles <- system.file("extdata", package = "iscream") |>
diff --git a/man/region_map.Rd b/man/region_map.Rd
index f2a035f..d1b6b86 100644
--- a/man/region_map.Rd
+++ b/man/region_map.Rd
@@ -17,15 +17,16 @@ region_map(bedfiles, regions, fun = "aggregate", mval = TRUE, nthreads = NULL)
 or use the beta value
 when applying the function.}
 
-\item{nthreads}{Set number of threads to use. Should not be necessary as this
-is set by \code{option('iscream.threads')}}
+\item{nthreads}{Set number of threads to use overriding the
+\code{"iscream.threads"} option. See \code{?set_threads} for more information.}
 }
 \value{
 A data.frame
 }
 \description{
 Run a function on the CpGs in bedfiles across genomic regions. Currently
-supported functions are aggregate and average.
+supported functions are aggregate and average. Parallelized across files
+using threads from the \code{"iscream.threads"} option.
 }
 \details{
 Available functions:
diff --git a/man/set_threads.Rd b/man/set_threads.Rd
index 7677429..19220e5 100644
--- a/man/set_threads.Rd
+++ b/man/set_threads.Rd
@@ -43,11 +43,12 @@ available threads but it may not reliably report hyperthreading ('system' or
 \if{html}{\out{<div class="sourceCode">}}\preformatted{options(iscream.threads = [n_threads])
 }\if{html}{\out{</div>}}
 
-in your .Rprofile. See help('Rprofile') for information on startup options.
+in your \code{.Rprofile} See \code{help('Rprofile')} for information on startup options.
 
 Functions currently using OpenMP:
 \itemize{
 \item \code{region_map()}
+\item \code{query_all()}
 }
 }
 \examples{