@@ -1,6 +1,6 @@

 Package: fenr

 Title: Fast functional enrichment for interactive applications

-Version: 1.5.1

+Version: 1.5.2

 Authors@R: person(

     given = "Marek",

     family = "Gierlinski",

@@ -173,4 +173,8 @@

 ## Version 1.4.1

- - Attempted to fix a bizarre error message on Bioconductor's test machines with older version of MacOS. Windows and Linux are not affected; my laptop running Sequoia 5.2 does not show show errors. I suspect a memory leak in older systems. The error `vector memory limit of 64.0 Gb reached, see mem.maxVSize()` happened in the function parse_kegg_genes(), a flat-file parser for KEGG. It occurred around the call tidyr::separate(), which I replaced with an alternative approach. Will see if the error is fixed.

\ No newline at end of file

+ - Attempted to fix a bizarre error message on Bioconductor's test machines with older version of MacOS. Windows and Linux are not affected; my laptop running Sequoia 5.2 does not show show errors. I suspect a memory leak in older systems. The error `vector memory limit of 64.0 Gb reached, see mem.maxVSize()` happened in the function parse_kegg_genes(), a flat-file parser for KEGG. It occurred around the call tidyr::separate(), which I replaced with an alternative approach. Will see if the error is fixed.

+

+ ## Version 1.4.2

+

+ - Added evidence code column to GO-term mapping table. It can be used to filter mapping based on their quality. See https://geneontology.org/docs/guide-go-evidence-codes for explanation.

\ No newline at end of file

@@ -48,6 +48,7 @@ stringr::str_glue("

     <Attribute name = 'ensembl_gene_id'/>

     <Attribute name = 'external_gene_name'/>

     <Attribute name = 'go_id'/>

+    <Attribute name = 'go_linkage_type'/>

   </Dataset>

 </Query>") |>

     stringr::str_replace_all("\n", "") |>

@@ -195,12 +196,13 @@ fetch_go_species <- function(on_error = c("stop", "warn", "ignore")) {

 #'   either "stop" to halt execution, "warn" to issue a warning and return

 #'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".

 #'

-#' @return A tibble with columns \code{gene_symbol}, \code{uniprot_id} and \code{term_id}.

+#' @return A tibble with columns \code{gene_symbol}, \code{uniprot_id}, 

+#'   \code{term_id} and \code{evidence}.

 #' @noRd

 fetch_go_genes_go <- function(species, use_cache, on_error) {

   # Binding variables from non-standard evaluation locally

   gene_id <- db_object_synonym <- symbol <- NULL

-  db_id <- go_term <- NULL

+  db_id <- go_term <- evidence <- NULL

   url <- get_go_annotation_url()

   if(!assert_url_path(url, on_error))

@@ -211,7 +213,7 @@ fetch_go_genes_go <- function(species, use_cache, on_error) {

   readr::read_tsv(lpath, comment = "!", quote = "", col_names = GAF_COLUMNS,

                   col_types = GAF_TYPES) |>

     dplyr::mutate(gene_id = stringr::str_remove(db_object_synonym, "\\|.*$")) |>

-    dplyr::select(gene_symbol = symbol, gene_id, db_id, term_id = go_term) |>

+    dplyr::select(gene_symbol = symbol, gene_id, db_id, term_id = go_term, evidence) |>

     dplyr::distinct()

 }

@@ -272,8 +274,8 @@ fetch_go_from_go <- function(species, use_cache, on_error) {

 #'   either "stop" to halt execution, "warn" to issue a warning and return

 #'   `NULL` or "ignore" to return `NULL` without warnings. Defaults to "stop".

 #'

-#' @return A tibble with columns \code{gene_id}, \code{gene_symbol} and

-#'   \code{term_id}.

+#' @return A tibble with columns \code{gene_id}, \code{gene_symbol},

+#'   \code{term_id} and \code{evidence}.

 #' @noRd

 fetch_go_genes_bm <- function(dataset, use_cache, on_error) {

   xml <- get_biomart_xml(dataset) |>

@@ -287,8 +289,8 @@ fetch_go_genes_bm <- function(dataset, use_cache, on_error) {

   # Problems with cache, bfcneedsupdate returns error for this query

   # lpath <- cached_url_path(stringr::str_glue("biomart_{dataset}"), resp, use_cache)

   res <- readr::read_tsv(req, show_col_types = FALSE)

-  if(ncol(res) == 3) {

-    res |> rlang::set_names(c("gene_id", "gene_symbol", "term_id"))

+  if(ncol(res) == 4) {

+    res |> rlang::set_names(c("gene_id", "gene_symbol", "term_id", "evidence"))

   } else {

     error_response("Problem with Biomart", on_error)

   }

Binary files a/data/go.rda and b/data/go.rda differ

@@ -98,6 +98,8 @@ The second tibble contains gene-term mapping:

 go$mapping

 ```

+Note that the mapping can be filtered based on the [evidence code](https://geneontology.org/docs/guide-go-evidence-codes/) (column `evidence`) to include only high-quality GO annotations, before further analysis. Here, we simply use all annotations.

+

 To make these user-friendly data more suitable for rapid functional enrichment analysis, they need to be converted into a machine-friendly object using the following function:

 ```{r prepare_for_enrichment}