@@ -14,6 +14,7 @@ Encoding: UTF-8

 LazyData: true

 biocViews:

 Imports:

+    assertthat,

     stats,

     dplyr,

     httr,

@@ -5,7 +5,9 @@ export(fetch_go_from_bm)

 export(fetch_go_from_go)

 export(fetch_go_species)

 export(fetch_kegg)

+export(fetch_kegg_species)

 export(fetch_reactome)

 export(fetch_reactome_species)

 export(functional_enrichment)

 export(prepare_for_enrichment)

+import(assertthat)

@@ -1,3 +1,14 @@

+#' Find all species available from KEGG

+#'

+#' @return A tibble, in which column \code{organism} contains species

+#'   designations used in function \code{fetch_kegg}.

+#' @export

+fetch_kegg_species <- function() {

+  KEGGREST::keggList("organism") |>

+    tibble::as_tibble()

+}

+

+

 #' Get functional term data from KEGG

 #'

 #' Download information (pathway ID and name) and gene-pathway mapping (entrez

@@ -7,21 +18,29 @@

 #' based on BioConductor package \pkg{KEGGREST}.

 #'

 #' @param species KEGG species code, for example "hsa" for human. The

-#'   full list of available KEGG species can be found by using

-#'   \code{KEGGREST::keggList("organism")}. The column \code{organism} contains

-#'   the codes used here.

-#' @param batch_size Nubmer of pathways sent to KEGG database in one query. The

+#'   full list of available KEGG species can be found by using \code{fetch_kegg_species}.

+#' @param batch_size Number of pathways sent to KEGG database in one query. The

 #'   maximum allowed is 10.

 #'

 #' @return A list with \code{terms} and \code{mapping} tibbles.

 #' @export

+#' @import assertthat

 #'

 #' @examples

 #' \dontrun{

 #' kegg_data <- fetch_kegg("hsa")

 #' }

 fetch_kegg <- function(species, batch_size = 10) {

-  lst <- KEGGREST::keggList("pathway", species)

+  assert_that(is.string(species))

+  assert_that(is.count(batch_size))

+  assert_that(batch_size <= 10, msg = "batch_size needs to be between 1 and 10")

+

+  lst <- tryCatch(

+    KEGGREST::keggList("pathway", species),

+    error = function(err)

+      stop(stringr::str_glue("There is a problem retrieving KEGG pathways for species '{species}'."))

+  )

+

   terms <- tibble::tibble(

     term_id = names(lst) |> stringr::str_remove("path:"),

     term_name = lst

@@ -31,7 +50,11 @@ fetch_kegg <- function(species, batch_size = 10) {

   pb <- progress::progress_bar$new(total = length(batches))

   mapping <- purrr::map_dfr(batches, function(batch) {

-    pws <- KEGGREST::keggGet(batch)

+    pws <- tryCatch(

+      KEGGREST::keggGet(batch),

+      error = function(err)

+        stop(stringr::str_glue("There is a problem retrieving KEGG batch':\n{err}"))

+    )

     pb$tick()

     purrr::map_dfr(pws, function(pw) {

       if (!is.null(pw$GENE)) {

@@ -8,11 +8,9 @@ fetch_kegg(species, batch_size = 10)

 }

 \arguments{

 \item{species}{KEGG species code, for example "hsa" for human. The

-full list of available KEGG species can be found by using

-\code{KEGGREST::keggList("organism")}. The column \code{organism} contains

-the codes used here.}

+full list of available KEGG species can be found by using \code{fetch_kegg_species}.}

-\item{batch_size}{Nubmer of pathways sent to KEGG database in one query. The

+\item{batch_size}{Number of pathways sent to KEGG database in one query. The

 maximum allowed is 10.}

 }

 \value{

new file mode 100644

@@ -0,0 +1,15 @@

+% Generated by roxygen2: do not edit by hand

+% Please edit documentation in R/kegg.R

+\name{fetch_kegg_species}

+\alias{fetch_kegg_species}

+\title{Find all species available from KEGG}

+\usage{

+fetch_kegg_species()

+}

+\value{

+A tibble, in which column \code{organism} contains species

+  designations used in function \code{fetch_kegg}.

+}

+\description{

+Find all species available from KEGG

+}