diff --git a/.bumpversion.cfg b/.bumpversion.cfg index 198491e4..0bfb2ef7 100644 --- a/.bumpversion.cfg +++ b/.bumpversion.cfg @@ -1,5 +1,5 @@ [bumpversion] -current_version = 3.9.11 +current_version = 3.11.1 commit = True tag = True files = DESCRIPTION diff --git a/R/interactions.R b/R/interactions.R index 9a2747f4..50f126d8 100644 --- a/R/interactions.R +++ b/R/interactions.R @@ -1155,6 +1155,8 @@ import_small_molecule_protein_interactions <- function( #' @param strict_evidences Logical: restrict the evidences to the queried #' datasets and resources. If set to FALSE, the directions and effect signs #' and references might be based on other datasets and resources. +#' @param types Character: interaction types, such as "transcriptional", +#' "post_transcriptional", "post_translational", etc. #' @param ... optional additional arguments #' #' @examples @@ -1182,15 +1184,13 @@ import_all_interactions <- function( default_fields = TRUE, references_by_resource = TRUE, strict_evidences = FALSE, + types = NULL, ... ){ - all_datasets <- - omnipath_url('queries/interactions?format=json') %>% - safe_json(path = .) %>% - extract2('datasets') %>% - setdiff(exclude) - + q_info <- query_info('interactions') + datasets <- q_info %>% extract2('datasets') %>% setdiff(exclude) + types %<>% if_null(q_info %>% extract2('types')) # it does not make sense without the type field fields %<>% c('type', 'dorothea_level') %>% unique @@ -1200,7 +1200,8 @@ import_all_interactions <- function( organism = organism, dorothea_levels = dorothea_levels, exclude = exclude, - datasets = all_datasets, + datasets = datasets, + types = types, fields = fields, default_fields = default_fields, references_by_resource = references_by_resource, diff --git a/R/resources.R b/R/resources.R index 58b1d1da..226d9210 100644 --- a/R/resources.R +++ b/R/resources.R @@ -272,7 +272,7 @@ query_info <- function(query_type) { #' otherwise a data frame. #' #' @examples -#' database_summary('annotations') +#' annotations_summary <- database_summary('annotations') #' #' @importFrom magrittr %>% #' @importFrom purrr map keep diff --git a/docs/reference/all_uniprots.html b/docs/reference/all_uniprots.html index cb7272d5..398792ac 100644 --- a/docs/reference/all_uniprots.html +++ b/docs/reference/all_uniprots.html @@ -16,7 +16,7 @@ OmnipathR - 3.9.6 + 3.9.7