Add return value to all docs

R/chromosome-map.R

@@ -25,6 +25,9 @@
 #' @param ... <[`dynamic-dots`][rlang::dyn-dots]> Additional arguments passed to
 #'   internal plotting functions.
 #'
+#' @return A [chromoMap][chromoMap::chromoMap] or
+#'   [karyoploteR](https://bernatgel.github.io/karyoploter_tutorial/) object.
+#'
 #' @seealso See the [chromoMap][chromoMap::chromoMap] and
 #'   [karyoploteR](https://bernatgel.github.io/karyoploter_tutorial/) packages
 #'   to create custom chromosome maps.

R/convert.R

@@ -7,7 +7,9 @@
 #' Conversion is case-insensitive, but always returns capitalized 1-letter and
 #' 3-letter abbreviations in title-case.
 #'
-#' @param str String containing amino acids to convert.
+#' @param str Character vector containing amino acids to convert.
+#'
+#' @return Character vector with converted amino acid abbreviations.
 #'
 #' @aliases convert
 #' @export

R/example.R

@@ -6,6 +6,8 @@
 #'
 #' @param path Name of file. If `NULL`, all example files will be listed.
 #'
+#' @return A local filepath or a list of all available files.
+#'
 #' @aliases example
 #' @export
 #' @examples

R/filter.R

@@ -62,10 +62,19 @@ filter_fn_factory <- function(.col, .type = c("numeric", "character")) {
 #'
 #' @param .data A data frame, data frame extension (e.g. a tibble), or a lazy
 #'   data frame (e.g. from dbplyr or dtplyr).
-#' @param .value Filtering value. Data greater than or equal to the value will
-#'   be kept.
+#' @param .value Filtering value. If a number, data greater than or equal to the
+#'   value will be kept. If a string, data equal to the value will be kept.
 #' @inheritParams dplyr::filter
 #'
+#' @return
+#' An object of the same type as `.data`. The output has the following
+#' properties:
+#'
+#' * Rows are a subset of the input, but appear in the same order.
+#' * Columns are not modified.
+#' * The number of groups may be reduced (if `.preserve` is not `TRUE`).
+#' * Data frame attributes are preserved.
+#'
 #' @name filter
 #' @seealso [dplyr::filter()] for more complex filtering operations.
 #' @examples

R/mutation-frequency.R

@@ -109,6 +109,8 @@ mutation_frequency.ref_alt_cov_tbl <- function(data, threshold) {
 #'   of [mutation_frequency()].
 #' @param ...	Other arguments passed to specific methods.
 #'
+#' @return A [ggplot2][ggplot2::ggplot2-package] object.
+#'
 #' @export
 #' @seealso [mutation_frequency()] for generating the data for plotting.
 #' @examples

R/mutation-prevalence.R

@@ -143,6 +143,8 @@ mutation_prevalence.geno_tbl <- function(data, ...) {
 #'   of [mutation_prevalence()].
 #' @param ...	Other arguments passed to specific methods.
 #'
+#' @return A [ggplot2][ggplot2::ggplot2-package] object.
+#'
 #' @export
 #' @seealso [mutation_prevalence()] for generating the data for plotting.
 #' @examples

R/plot_coverage.R

@@ -10,6 +10,8 @@
 #' @param group_by The grouping variable. The average coverage is computed for
 #'   each unique value of the variable.
 #'
+#' @return A [ggplot2][ggplot2::ggplot2-package] object.
+#'
 #' @export
 #' @examples
 #' # Read example data

R/read-tbl.R

@@ -17,7 +17,7 @@
 #' sequenced.
 #'
 #' @section Useful filter functions:
-#' The [dplyr::filter()] function is employed to subset the rows of the data
+#' The [dplyr::filter()] function is employed to subset the rows of the data by
 #' applying the expressions in `...` to the column values to determine which
 #' rows should be retained.
 #'
@@ -47,11 +47,9 @@
 #' @param gene `r lifecycle::badge("deprecated")` The gene(s) to filter to.
 #'
 #' @return
-#' A [`tibble()`][tibble::tibble-package]. The first six columns contain the
-#' metadata associated with each sample and mutation. The last column contains
-#' the information parsed from the table. In some cases, this may be the
-#' umi_count and in other cases it may be the coverage of the associated data
-#' point.
+#' A [`tibble()`][tibble::tibble-package] subclass. Each function defines a
+#' unique subclass to store the data. Data typically contains the sample,
+#' associated metadata, and the value of interest.
 #'
 #' @seealso [vroom::vroom()] [dplyr::filter()]
 #' @name read-tbl

R/themes.R

@@ -9,6 +9,8 @@
 #' @param base_line_size Base size for line elements.
 #' @param base_rect_size Base size for rect elements.
 #'
+#' @return A [ggplot2][ggplot2::theme] theme.
+#'
 #' @importFrom ggplot2 %+replace%
 #' @examples
 #' library("ggplot2")