docs(threads): add query_all as OpenMP func; update nthread docs

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
 #'

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

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
 #'