BiocCheck

Author: multimeric

NAMESPACE

@@ -1,8 +1,10 @@
 # Generated by roxygen2: do not edit by hand
 
 S3method(as.sparse,DelayedMatrix)
+export("=")
+export("SAMPLE_DATABASE_URL)")
+export("get_metadata(remote_url")
 export(DATABASE_URL)
-export(SAMPLE_DATABASE_URL)
 export(get_SingleCellExperiment)
 export(get_metadata)
 export(get_seurat)

R/metadata.R

@@ -10,6 +10,8 @@ cache <- rlang::env(
 
 #' URL pointing to the full metadata file
 #' @export
+#' @examples
+#' get_metadata(remote_url = DATABASE_URL)
 DATABASE_URL <- single_line_str(
     "https://object-store.rc.nectar.org.au/v1/
     AUTH_06d6e008e3e642da99d806ba3ea629c5/metadata/metadata.0.2.3.parquet"
@@ -18,6 +20,7 @@ DATABASE_URL <- single_line_str(
 #' URL pointing to the sample metadata file, which is smaller and for test,
 #' demonstration, and vignette purposes only
 #' @export
+#' get_metadata(remote_url = SAMPLE_DATABASE_URL)
 SAMPLE_DATABASE_URL <- single_line_str(
     "https://object-store.rc.nectar.org.au/v1/
     AUTH_06d6e008e3e642da99d806ba3ea629c5/metadata/

R/unharmonised.R

@@ -37,11 +37,11 @@ UNHARMONISED_URL <- single_line_str(
 #'   a "lazy data frame", ie a `tbl`.
 #' @examples
 #' \donttest{
-#' dataset = "838ea006-2369-4e2c-b426-b2a744a2b02b"
-#' harmonised_meta = get_metadata() |> 
+#' dataset <- "838ea006-2369-4e2c-b426-b2a744a2b02b"
+#' harmonised_meta <- get_metadata() |> 
 #'     dplyr::filter(file_id == dataset) |> dplyr::collect()
-#' unharmonised_meta = get_unharmonised_dataset(dataset)
-#' unharmonised_tbl = dplyr::collect(unharmonised_meta[[dataset]])
+#' unharmonised_meta <- get_unharmonised_dataset(dataset)
+#' unharmonised_tbl <- dplyr::collect(unharmonised_meta[[dataset]])
 #' dplyr::left_join(harmonised_meta, unharmonised_tbl, by=c("file_id", "cell_"))
 #' }
 get_unharmonised_dataset <- function(
@@ -84,7 +84,7 @@ get_unharmonised_dataset <- function(
 #' @examples
 #' harmonised <- dplyr::filter(get_metadata(), tissue == "kidney blood vessel")
 #' unharmonised <- get_unharmonised_metadata(harmonised)
-get_unharmonised_metadata = function(metadata, ...){
+get_unharmonised_metadata <- function(metadata, ...){
     args <- list(...)
     metadata |>
         collect() |>