diff --git a/R/jaspar.R b/R/jaspar.R index 17202991..48923b49 100644 --- a/R/jaspar.R +++ b/R/jaspar.R @@ -12,7 +12,7 @@ #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/collections/" +#' "GET https://jaspar.elixir.no/api/v1/collections/" #' #' @return A data frame with collections' names and URLs. #' @@ -109,7 +109,7 @@ rba_jaspar_collections <- function(release = 2024, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/collections/{collection}/" +#' "GET https://jaspar.elixir.no/api/v1/collections/\{collection\}/" #' #' @return A list that contains a data frame with information of matrix #' profiles available in the collection. @@ -262,7 +262,7 @@ rba_jaspar_collections_matrices <- function(collection, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/api/v1/matrix/" +#' "GET https://jaspar.elixir.no/api/v1/api/v1/matrix/" #' #' @return A list that contains a data frame of matrix profiles' information. #' @@ -429,7 +429,7 @@ rba_jaspar_matrix_search <- function(term = NULL, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/matrix/{base_id}/versions/" +#' "GET https://jaspar.elixir.no/api/v1/matrix/\{base_id\}/versions/" #' #' @return A data frame of matrix profiles' versions information. #' @@ -520,7 +520,7 @@ rba_jaspar_matrix_versions <- function(base_id, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/matrix/{matrix_id}/" +#' "GET https://jaspar.elixir.no/api/v1/matrix/\{matrix_id\}/" #' #' @return A list that contains the PFM along with its details and #' annotations. If file_format was supplied, an un-parsed character string @@ -638,8 +638,8 @@ rba_jaspar_matrix <- function(matrix_id, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/releases/" -#' "GET "https://jaspar.elixir.no/api/v1/releases/{release_number}/" +#' "GET https://jaspar.elixir.no/api/v1/releases/" +#' \cr "GET https://jaspar.elixir.no/api/v1/releases/\{release_number\}/" #' #' @return A list that contains all JASPAR database releases' information or #' details of a particular release. @@ -731,7 +731,7 @@ rba_jaspar_releases <- function(release_number = NULL, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/sites/{matrix_id}/" +#' "GET https://jaspar.elixir.no/api/v1/sites/\{matrix_id\}/" #' #' @return A list that contains a data frame with binding sites information. #' @@ -809,7 +809,7 @@ rba_jaspar_sites <- function(matrix_id, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/species/" +#' "GET https://jaspar.elixir.no/api/v1/species/" #' #' @return A data frame with information of available species. #' @@ -918,7 +918,7 @@ rba_jaspar_species <- function(release = 2024, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/species/{tax_id}/" +#' "GET https://jaspar.elixir.no/api/v1/species/\{tax_id\}/" #' #' @return A list that contains a data frame with information of matrix #' profiles available for the species. @@ -1026,7 +1026,7 @@ rba_jaspar_species_matrices <- function(tax_id, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/taxon/" +#' "GET https://jaspar.elixir.no/api/v1/taxon/" #' #' @return A data frame with information of available species. #' @@ -1122,7 +1122,7 @@ rba_jaspar_taxons <- function(release = 2024, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/taxon/{tax_group}/" +#' "GET https://jaspar.elixir.no/api/v1/taxon/\{tax_group\}/" #' #' @return A list that contains a data frame with information of matrix #' profiles available for the taxonomic group. @@ -1261,7 +1261,7 @@ rba_jaspar_taxons_matrices <- function(tax_group, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/api/v1/tffm/" +#' "GET https://jaspar.elixir.no/api/v1/api/v1/tffm/" #' #' @return A list that contains a data frame with information of query hits' #' TFFMs. @@ -1376,7 +1376,7 @@ rba_jaspar_tffm_search <- function(term = NULL, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://jaspar.elixir.no/api/v1/fttm/{tffm_id}/" +#' "GET https://jaspar.elixir.no/api/v1/fttm/\{tffm_id\}/" #' #' @return A list that contains the TFFM's information and annotations. #' diff --git a/R/mieaa.R b/R/mieaa.R index b0f1b314..7ad421dc 100644 --- a/R/mieaa.R +++ b/R/mieaa.R @@ -87,7 +87,7 @@ #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET "https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_categories/{species}/{mirna_type}/" +#' "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_categories/\{species\}/\{mirna_type\}/" #' #' @return a named character vector with the supported categories for #' your supplied input combination. @@ -442,7 +442,7 @@ rba_mieaa_convert_type <- function(mirna, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "POST https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_analysis/{species}/{type}/{test}/" +#' "POST https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_analysis/\{species\}/\{type\}/\{test\}/" #' #' @return A list that contains your submitted job's ID and a URL to #' manually check for your job status. @@ -605,7 +605,7 @@ rba_mieaa_enrich_submit <- function(test_set, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/job_status/{job_id}" +#' "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/job_status/\{job_id\}" #' #' @return A list containing the status value for a analysis that corresponds #' to your supplied job-id. @@ -679,7 +679,7 @@ rba_mieaa_enrich_status <- function(job_id, ...) { #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/results/{job_id}" +#' "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/results/\{job_id\}" #' #' @return A data frame with your enrichment analysis results. #' diff --git a/R/reactome_analysis.R b/R/reactome_analysis.R index 0e8d809f..2865856b 100644 --- a/R/reactome_analysis.R +++ b/R/reactome_analysis.R @@ -379,8 +379,8 @@ rba_reactome_analysis <- function(input, #' in other formats. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/AnalysisService/report/{token}/{species}/ -#' {filename}.pdf" +#' "GET https://reactome.org/AnalysisService/report/\{token\}/\{species\}/ +#' \{filename\}.pdf" #' #' @param token A token associated to your previous Reactome analysis. #' @param species Numeric or Character: NCBI Taxonomy identifier (Human Taxonomy @@ -547,14 +547,14 @@ rba_reactome_analysis_pdf <- function(token, #' in PDF format. #' #' @section Corresponding API Resources: -#' GET https://reactome.org/AnalysisService/download/{token}/entities/ -#' found/{resource}/{filename}.csv" -#' GET https://reactome.org/AnalysisService//download/{token}/entities/ -#' notfound/{filename}.csv" -#' GET https://reactome.org/AnalysisService/download/{token}/pathways/ -#' {resource}/{filename}.csv" -#' GET https://reactome.org/AnalysisService/download/{token}/result.json" -#' GET https://reactome.org/AnalysisService/download/{token}/result.json.gz" +#' GET https://reactome.org/AnalysisService/download/\{token\}/entities/ +#' found/\{resource\}/\{filename\}.csv" +#' \cr GET https://reactome.org/AnalysisService/download/\{token\}/entities/ +#' notfound/\{filename\}.csv" +#' \cr GET https://reactome.org/AnalysisService/download/\{token\}/pathways/ +#' \{resource\}/\{filename\}.csv" +#' \cr GET https://reactome.org/AnalysisService/download/\{token\}/result.json" +#' \cr GET https://reactome.org/AnalysisService/download/\{token\}/result.json.gz" #' #' @param token A token associated to your previous Reactome analysis. #' @param request What to download? Should be one of:\itemize{ @@ -938,7 +938,7 @@ rba_reactome_analysis_mapping <- function(input, #' Reactome Computationally Inferred Events} for more information. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/AnalysisService/species/homoSapiens/{species}" +#' "GET https://reactome.org/AnalysisService/species/homoSapiens/\{species\}" #' #' @param species_dbid Numeric: Reactome DbId (e.g Mus musculus is 48892) of #' the species you want to compare with Homo sapiens. See @@ -1093,7 +1093,7 @@ rba_reactome_analysis_species <- function(species_dbid, #' reactome (using \code{\link{rba_reactome_analysis_import}}) to generate #' a new token. #' @section Corresponding API Resources: -#' "GET https://reactome.org/AnalysisService/token/{token}" +#' "GET https://reactome.org/AnalysisService/token/\{token\}" #' #' @param token A token associated to your previous Reactome analysis. #' @param species Numeric or Character: NCBI Taxonomy identifier (Human diff --git a/R/reactome_content.R b/R/reactome_content.R index 7b3f543f..b3ef9a07 100644 --- a/R/reactome_content.R +++ b/R/reactome_content.R @@ -68,8 +68,8 @@ rba_reactome_version <- function(...) { #' Reactome. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/GET data/diseases" -#' "GET https://reactome.org/ContentService/GET data/diseases/doid" +#' "GET https://reactome.org/ContentService/data/diseases" +#' \cr "GET https://reactome.org/ContentService/data/diseases/doid" #' #' @param doid (logical) Return disease DOIDs instead of diseases? #' (default = FALSE) @@ -159,7 +159,7 @@ rba_reactome_diseases <- function(doid = FALSE, #' results. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/complex/{id}/subunits" +#' "GET https://reactome.org/ContentService/data/complex/\{id\}/subunits" #' #' @param complex_id Reactome stable Identifier of the complex. #' @param exclude_structures (logical) Should the contained complexes and @@ -241,8 +241,8 @@ rba_reactome_complex_subunits <- function(complex_id, #' molecule as a component. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/complexes/{resource}/ -#' {identifier}" +#' "GET https://reactome.org/ContentService/data/complexes/\{resource\}/ +#' \{identifier\}" #' #' @param id Molecule's external Identifier #' @param resource What is the resource of your supplied ID? see: @@ -321,7 +321,7 @@ rba_reactome_complex_list <- function(id, #' reaction output). #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/entity/{id}/componentOf" +#' "GET https://reactome.org/ContentService/data/entity/\{id\}/componentOf" #' #' @param entity_id Reactome's entity ID. #' @param ... rbioapi option(s). See \code{\link{rba_options}}'s @@ -393,7 +393,7 @@ rba_reactome_participant_of <- function(entity_id, #' H93R R-HSA-2318524 and PTEN C124R R-HSA-2317439 are two forms of PTEN." #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/entity/{id}/otherForms" +#' "GET https://reactome.org/ContentService/data/entity/\{id\}/otherForms" #' #' @param entity_id Reactome's entity ID. #' @param ... rbioapi option(s). See \code{\link{rba_options}}'s @@ -469,7 +469,7 @@ rba_reactome_entity_other_forms <- function(entity_id, #' that a given event could be part of more that one hierarchies. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/event/{id}/ancestors" +#' "GET https://reactome.org/ContentService/data/event/\{id\}/ancestors" #' #' @param event_id Reactome event's identifier. #' @param ... rbioapi option(s). See \code{\link{rba_options}}'s @@ -547,7 +547,7 @@ rba_reactome_event_ancestors <- function(event_id, #' that a given event could be part of more that one hierarchies. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/eventsHierarchy/{species}" +#' "GET https://reactome.org/ContentService/data/eventsHierarchy/\{species\}" #' #' @param species Numeric or Character: NCBI Taxonomy identifier (Human Taxonomy #' ID is 9606.) or species name (e.g. "Homo sapiens"). See @@ -645,10 +645,10 @@ rba_reactome_event_hierarchy <- function(species, #' of your supplied event's children will also be included. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/exporter/diagram/{identifier} -#' .{ext}" -#' "GET https://reactome.org/ContentService/exporter/document/event/ -#' {identifier}.pdf" +#' "GET https://reactome.org/ContentService/exporter/diagram/\{identifier\} +#' .\{ext\}" +#' \cr "GET https://reactome.org/ContentService/exporter/document/event/ +#' \{identifier\}.pdf" #' #' @param event_id Reactome event's identifier. #' @param save_to NULL or Character:\itemize{ @@ -903,10 +903,10 @@ rba_reactome_exporter_diagram <- function(event_id, #' arguments manual for more information on available options. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService//exporter/event/ -#' {identifier}.sbgn" -#' "GET https://reactome.org/ContentService//exporter/event/ -#' {identifier}.sbml" +#' "GET https://reactome.org/ContentService/exporter/event/ +#' \{identifier\}.sbgn" +#' \cr "GET https://reactome.org/ContentService/exporter/event/ +#' \{identifier\}.sbml" #' #' @return NULL, According to the inputs, a SBGN or SBML file will be saved to #' disk. @@ -987,7 +987,7 @@ rba_reactome_exporter_event <- function(event_id, #' as an image file. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/exporter/fireworks/{species}.{ext}" +#' "GET https://reactome.org/ContentService/exporter/fireworks/\{species\}.\{ext\}" #' #' @param species Numeric or Character: NCBI Taxonomy identifier (Human Taxonomy #' ID is 9606.) or species name (e.g. "Homo sapiens"). See @@ -1199,8 +1199,8 @@ rba_reactome_exporter_overview <- function(species, #' pathway, use \code{\link{rba_reactome_exporter_diagram}}. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService//exporter/reaction/ -#' {identifier}.{ext}" +#' "GET https://reactome.org/ContentService/exporter/reaction/ +#' \{identifier\}.\{ext\}" #' #' @param event_id Reactome #' \href{https://reactome.org/content/schema/ReactionLikeEvent/}{Reaction-like @@ -1413,10 +1413,10 @@ rba_reactome_exporter_reaction <- function(event_id, #' #' @section Corresponding API Resources: #' "POST https://reactome.org/ContentService/interactors/psicquic/molecules/ -#' {resource}/details" -#' "POST https://reactome.org/ContentService/interactors/psicquic/molecules/ -#' {resource}/summary" -#' "GET https://reactome.org/ContentService/interactors/psicquic/resources" +#' \{resource\}/details" +#' \cr "POST https://reactome.org/ContentService/interactors/psicquic/molecules/ +#' \{resource\}/summary" +#' \cr "GET https://reactome.org/ContentService/interactors/psicquic/resources" #' #' @param proteins Proteins to retrieve PSICQUIC interactors. #' @param resource The PSICQUIC resource for your supplied proteins. Call @@ -1677,10 +1677,10 @@ rba_reactome_interactors_static <- function(proteins, #' a list of pathways/reactions that include your supplied ID. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/mapping/{resource}/ -#' {identifier}/pathways" -#' \cr "GET https://reactome.org/ContentService/data/mapping/{resource}/ -#' {identifier}/reactions" +#' "GET https://reactome.org/ContentService/data/mapping/\{resource\}/ +#' \{identifier\}/pathways" +#' \cr "GET https://reactome.org/ContentService/data/mapping/\{resource\}/ +#' \{identifier\}/reactions" #' #' @param id Molecule's external Identifier #' @param resource What is the resource of your supplied ID? see: @@ -1789,7 +1789,7 @@ rba_reactome_mapping <- function(id, #' #' @section Corresponding API Resources: #' "POST https://reactome.org/ContentService/data/orthologies/ids/ -#' species/{speciesId}" +#' species/\{speciesId\}" #' #' @param event_ids Human Reactome event ID(s) to retrieve their orthologous #' events. @@ -1900,10 +1900,10 @@ rba_reactome_orthology <- function(event_ids, #' Entities. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/participants/{id}" -#' \cr "GET https://reactome.org/ContentService/data/participants/{id}/ +#' "GET https://reactome.org/ContentService/data/participants/\{id\}" +#' \cr "GET https://reactome.org/ContentService/data/participants/\{id\}/ #' participatingPhysicalEntities" -#' \cr "GET https://reactome.org/ContentService/data/participants/{id}/ +#' \cr "GET https://reactome.org/ContentService/data/participants/\{id\}/ #' referenceEntities" #' #' @param event_id Reactome event's database ID (DbId) or Stable ID (StId). @@ -2019,10 +2019,10 @@ rba_reactome_participants <- function(event_id, #' that a given event could be part of more that one hierarchies. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/pathway/{id}/ +#' "GET https://reactome.org/ContentService/data/pathway/\{id\}/ #' containedEvents" -#' \cr "GET https://reactome.org/ContentService/data/pathway/{id}/ -#' containedEvents/{attributeName}" +#' \cr "GET https://reactome.org/ContentService/data/pathway/\{id\}/ +#' containedEvents/\{attributeName\}" #' #' @param event_id Reactome event's database ID (DbId) or Stable ID (StId). #' @param attribute_name An attribute of the events to be returned instead of @@ -2128,11 +2128,11 @@ rba_reactome_pathways_events <- function(event_id, #' modify your search. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/pathways/low/entity/{id}" +#' "GET https://reactome.org/ContentService/data/pathways/low/entity/\{id\}" #' \cr "GET https://reactome.org/ContentService/data/pathways/low/diagram/ -#' entity/{id}" +#' entity/\{id\}" #' \cr "GET https://reactome.org/ContentService/data/pathways/low/diagram/ -#' entity/{id}/allForms" +#' entity/\{id\}/allForms" #' #' @param entity_id The entity that should exist in the pathways. #' @param with_diagram Logical: only include pathways with diagram? @@ -2246,7 +2246,7 @@ rba_reactome_pathways_low <- function(entity_id, #' goes further down. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/pathways/top/{species}" +#' "GET https://reactome.org/ContentService/data/pathways/top/\{species\}" #' #' @param species Numeric or Character: NCBI Taxonomy identifier (Human Taxonomy #' ID is 9606.) or species name (e.g. "Homo sapiens"). See @@ -2329,8 +2329,8 @@ rba_reactome_pathways_top <- function(species, #' name and retrieve a list of matching people in Reactome. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/data/people/name/{name}" -#' \cr "GET https://reactome.org/ContentService/data/people/name/{name}/exact" +#' "GET https://reactome.org/ContentService/data/people/name/\{name\}" +#' \cr "GET https://reactome.org/ContentService/data/people/name/\{name\}/exact" #' #' @param person_name first and last name of the person #' @param exact_match Logical: should the supplied name be considered as @@ -2520,9 +2520,9 @@ rba_reactome_people_id <- function(person_id, #' @section Corresponding API Resources: #' "POST https://reactome.org/ContentService/data/query/ids" #' \cr "POST https://reactome.org/ContentService/data/query/ids/map" -#' \cr "GET https://reactome.org/ContentService/data/query/{id}" -#' \cr s"GET https://reactome.org/ContentService//data/query/enhanced/{id}" -#' \cr "GET https://reactome.org/ContentService/data/query/{id}/{attributeName}" +#' \cr "GET https://reactome.org/ContentService/data/query/\{id\}" +#' \cr "GET https://reactome.org/ContentService/data/query/enhanced/\{id\}" +#' \cr "GET https://reactome.org/ContentService/data/query/\{id\}/\{attributeName\}" #' #' @param ids A single or Multiple database IDs (DbId), Stable IDs (StId) or #' a mixture of both. @@ -2664,7 +2664,7 @@ rba_reactome_query <- function(ids, #' to learn more about how Reactome classifies molecules. #' #' @section Corresponding API Resources: -#' "GET https://reactome.org/ContentService/references/mapping/{identifier}" +#' "GET https://reactome.org/ContentService/references/mapping/\{identifier\}" #' #' @param xref_id molecule's cross-reference (external) identifier. #' @param ... rbioapi option(s). See \code{\link{rba_options}}'s diff --git a/R/stringdb.R b/R/stringdb.R index 974f7095..d543327f 100644 --- a/R/stringdb.R +++ b/R/stringdb.R @@ -7,8 +7,8 @@ #' with other STRING's functions. #' #' @section Corresponding API Resources: -#' "POST https://string-db.org/api/[output-format]/get_string_ids?identifiers= -#' [your_identifiers]&[optional_parameters]" +#' "POST https://string-db.org/api/\{output-format\}/get_string_ids?identifiers= +#' \{your_identifiers\}&\{optional_parameters\}" #' #' @param ids Your Common gene/protein Identifier(s) to be mapped. #' @param species Numeric: NCBI Taxonomy identifier; Human Taxonomy ID is 9606. @@ -105,8 +105,8 @@ rba_string_map_ids <- function(ids, #' image. #' #' @section Corresponding API Resources: -#' "POST https://string-db.org/api/[output-format]/network?identifiers= -#' [your_identifiers]&[optional_parameters]" +#' "POST https://string-db.org/api/\{output-format\}/network?identifiers= +#' \{your_identifiers\}&\{optional_parameters\}" #' #' @param ids Your protein ID(s). It is strongly recommended to supply #' STRING IDs. See \code{\link{rba_string_map_ids}} for more information. @@ -353,8 +353,8 @@ rba_string_network_image <- function(ids, #' \code{\link{rba_string_interaction_partners}}. #' #' @section Corresponding API Resources: -#' "POST https://string-db.org/api/[output-format]/network?identifiers= -#' [your_identifiers]&[optional_parameters]" +#' "POST https://string-db.org/api/\{output-format\}/network?identifiers= +#' \{your_identifiers\}&\{optional_parameters\}" #' #' @param ids Your protein IDs. It is strongly recommended to supply #' STRING IDs. See \code{\link{rba_string_map_ids}} for more information. @@ -516,8 +516,8 @@ rba_string_interactions_network <- function(ids, #' \code{\link{rba_string_interactions_network}}. #' #' @section Corresponding API Resources: -#' "POST https://string-db.org/api/[output-format]/ -#' interaction_partners?identifiers=[your_identifiers]&[optional_parameters]" +#' "POST https://string-db.org/api/\{output-format\}/ +#' interaction_partners?identifiers=\{your_identifiers\}&\{optional_parameters\}" #' #' @param ids Your protein ID(s). It is strongly recommended to supply #' STRING IDs. See \code{\link{rba_string_map_ids}} for more information. @@ -650,8 +650,8 @@ rba_string_interaction_partners <- function(ids, #' Proteins (SIMAP)} #' #' @section Corresponding API Resources: -#' "POST https://string-db.org/api/[output-format]/homology?identifiers= -#' [your_identifiers]" +#' "POST https://string-db.org/api/\{output-format\}/homology?identifiers= +#' \{your_identifiers\}" #' #' @param ids Your protein ID(s). It is strongly recommended to supply #' STRING IDs. See \code{\link{rba_string_map_ids}} for more information. @@ -748,8 +748,8 @@ rba_string_homology_intra <- function(ids, #' Proteins (SIMAP)} #' #' @section Corresponding API Resources: -#' "POST https://string-db.org/api/[output-format]/homology_best? -#' identifiers=[your_identifiers]" +#' "POST https://string-db.org/api/\{output-format\}/homology_best? +#' identifiers=\{your_identifiers\}" #' #' @param ids Your protein ID(s). It is strongly recommended to supply #' STRING IDs. See \code{\link{rba_string_map_ids}} for more information. @@ -857,8 +857,8 @@ rba_string_homology_inter <- function(ids, #' \code{\link{rba_string_annotations}}. #' #' @section Corresponding API Resources: -#' "POST https://string-db.org/api/[output_format]/enrichment?identifiers= -#' [your_identifiers]&[optional_parameters]" +#' "POST https://string-db.org/api/\{output_format\}/enrichment?identifiers= +#' \{your_identifiers\}&\{optional_parameters\}" #' #' @param ids Your protein ID(s). It is strongly recommended to supply #' STRING IDs. See \code{\link{rba_string_map_ids}} for more information. @@ -981,8 +981,8 @@ rba_string_enrichment <- function(ids, #' subset of the terms, use \code{\link{rba_string_enrichment}}. #' #' @section Corresponding API Resources: -#' "POST https://string-db.org/api/[output_format]/functional_annotation? -#' identifiers=[your_identifiers]&[optional_parameters]" +#' "POST https://string-db.org/api/\{output_format\}/functional_annotation? +#' identifiers=\{your_identifiers\}&\{optional_parameters\}" #' #' @param ids Your protein ID(s). It is strongly recommended to supply #' STRING IDs. See \code{\link{rba_string_map_ids}} for more information. @@ -1092,8 +1092,8 @@ rba_string_annotations <- function(ids, #' functionally related. #' #' @section Corresponding API Resources: -#' "POST https://string-db.org/api/[output_format]/ppi_enrichment?identifiers= -#' [your_identifiers]&[optional_parameters]" +#' "POST https://string-db.org/api/\{output_format\}/ppi_enrichment?identifiers= +#' \{your_identifiers\}&\{optional_parameters\}" #' #' @param ids Your protein ID(s). It is strongly recommended to supply #' STRING IDs. See \code{\link{rba_string_map_ids}} for more information. @@ -1202,7 +1202,7 @@ rba_string_enrichment_ppi <- function(ids, #' is outdated, Kindly contact me. #' #' @section Corresponding API Resources: -#' "GET https://string-db.org/api/[output_format]/version" +#' "GET https://string-db.org/api/\{output_format\}/version" #' #' @param ... rbioapi option(s). See \code{\link{rba_options}}'s #' arguments manual for more information on available options. diff --git a/R/uniprot_coordinates.R b/R/uniprot_coordinates.R index 38229df6..6f00ec30 100644 --- a/R/uniprot_coordinates.R +++ b/R/uniprot_coordinates.R @@ -153,8 +153,10 @@ rba_uniprot_coordinates_search <- function(accession = NULL, #' 40(6), 694–705. https://doi.org/10.1002/humu.23738 #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/coordinates/location/{accession}:{pPosition}" -#' \cr "GET https://ebi.ac.uk/proteins/api/coordinates/location/{accession}:{pStart}-{pEnd}" +#' "GET https://ebi.ac.uk/proteins/api/coordinates/location +#' /\{accession\}:\{pPosition\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/coordinates/location +#' /\{accession\}:\{pStart\}-\{pEnd\}" #' #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ #' UniProtKB primary or secondary accession}. @@ -254,8 +256,8 @@ rba_uniprot_coordinates_sequence <- function(accession, #' 40(6), 694–705. https://doi.org/10.1002/humu.23738 #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/coordinates/{accession}" -#' \cr "GET https://ebi.ac.uk/proteins/api/coordinates/{dbtype}:{dbid}" +#' "GET https://ebi.ac.uk/proteins/api/coordinates/\{accession\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/coordinates/\{dbtype\}:\{dbid\}" #' #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ #' UniProtKB primary or secondary accession}. @@ -351,8 +353,10 @@ rba_uniprot_coordinates <- function(accession = NULL, #' 40(6), 694–705. https://doi.org/10.1002/humu.23738 #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/coordinates/{taxonomy}/{locations}/feature" -#' \cr "GET https://ebi.ac.uk/proteins/api/coordinates/{taxonomy}/{locations}" +#' "GET https://ebi.ac.uk/proteins/api/coordinates +#' /\{taxonomy\}/\{locations\}/feature" +#' \cr "GET https://ebi.ac.uk/proteins/api/coordinates +#' /\{taxonomy\}/\{locations\}" #' #' @param taxid NIH-NCBI \href{https://www.uniprot.org/taxonomy/}{Taxon ID}. #' @param locations genomic location formatted as: chromosome:start-end. diff --git a/R/uniprot_proteins.R b/R/uniprot_proteins.R index 3e4a74a6..f51e14d8 100644 --- a/R/uniprot_proteins.R +++ b/R/uniprot_proteins.R @@ -264,9 +264,9 @@ rba_uniprot_proteins_search <- function(accession = NULL, #' TRUE, not both of them. #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/proteins/{accession}" -#' \cr "GET https://ebi.ac.uk/proteins/api/proteins/interaction/{accession}" -#' \cr "GET https://ebi.ac.uk/proteins/api/proteins/{accession}/isoforms" +#' "GET https://ebi.ac.uk/proteins/api/proteins/\{accession\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/proteins/interaction/\{accession\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/proteins/\{accession\}/isoforms" #' #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ #' UniProtKB primary or secondary accession}. @@ -365,7 +365,7 @@ rba_uniprot_proteins <- function(accession, #' and protein ID in that database. #' #' @section Corresponding API Resources: -#' "GET https://www.ebi.ac.uk/proteins/api/proteins/{dbtype}:{dbid}" +#' "GET https://www.ebi.ac.uk/proteins/api/proteins/\{dbtype\}:\{dbid\}" #' #' @param db_id The protein ID in the cross-reference (external) database. #' @param db_name \href{https://www.uniprot.org/database/}{cross-reference} @@ -832,7 +832,7 @@ rba_uniprot_features_search <- function(accession = NULL, #' (features)} of a protein by it's UniProt accession. #' #' @section Corresponding API Resources: -#' "GET https://www.ebi.ac.uk/proteins/api/features/{accession}" +#' "GET https://www.ebi.ac.uk/proteins/api/features/\{accession\}" #' #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ #' UniProtKB primary or secondary accession}. @@ -1212,9 +1212,9 @@ rba_uniprot_variation_search <- function(accession = NULL, #' accession, dbSNP or HGVS expression. #' #' @section Corresponding API Resources: -#' "GET https://www.ebi.ac.uk/proteins/api/variation/dbsnp/{dbid}" -#' \cr "GET https://www.ebi.ac.uk/proteins/api/variation/hgvs/{hgvs}" -#' \cr "GET https://www.ebi.ac.uk/proteins/api/variation/{accession}" +#' "GET https://www.ebi.ac.uk/proteins/api/variation/dbsnp/\{dbid\}" +#' \cr "GET https://www.ebi.ac.uk/proteins/api/variation/hgvs/\{hgvs\}" +#' \cr "GET https://www.ebi.ac.uk/proteins/api/variation/\{accession\}" #' #' @param id An ID which can be either a #' \href{https://www.uniprot.org/help/accession_numbers}{UniProt primary or @@ -1532,7 +1532,7 @@ rba_uniprot_proteomics_search <- function(accession = NULL, #' peptides features that has been map to a given UniProt protein's sequence. #' #' @section Corresponding API Resources: -#' "GET https://www.ebi.ac.uk/proteins/api/proteomics/{accession}" +#' "GET https://www.ebi.ac.uk/proteins/api/proteomics/\{accession\}" #' #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ #' UniProtKB primary or secondary accession}. @@ -1756,7 +1756,7 @@ rba_uniprot_ptm_search <- function(accession = NULL, #' Processing section in UniProtKB} #' #' @section Corresponding API Resources: -#' "GET https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}" +#' "GET https://www.ebi.ac.uk/proteins/api/proteomics-ptm/\{accession\}" #' #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ #' UniProtKB primary or secondary accession}. @@ -1940,7 +1940,7 @@ rba_uniprot_antigens_search <- function(accession = NULL, #' features that has been map to a given UniProt protein's sequence. #' #' @section Corresponding API Resources: -#' "GET https://www.ebi.ac.uk/proteins/api/antigen/{accession}" +#' "GET https://www.ebi.ac.uk/proteins/api/antigen/\{accession\}" #' #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ #' UniProtKB primary or secondary accession}(s). @@ -2115,7 +2115,7 @@ rba_uniprot_mutagenesis_search <- function(accession = NULL, #' Mutagenesis description} that has been mapped to a given UniProt protein. #' #' @section Corresponding API Resources: -#' "GET https://www.ebi.ac.uk/proteins/api/mutagenesis/{accession}" +#' "GET https://www.ebi.ac.uk/proteins/api/mutagenesis/\{accession\}" #' #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ #' UniProtKB primary or secondary accession}(s). diff --git a/R/uniprot_proteomes.R b/R/uniprot_proteomes.R index b81998e9..7f732ed9 100644 --- a/R/uniprot_proteomes.R +++ b/R/uniprot_proteomes.R @@ -174,8 +174,8 @@ rba_uniprot_proteomes_search <- function(name = NULL, #' proteomes?} for more information. #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/proteomes/proteins/{upid}" -#' \cr "GET https://ebi.ac.uk/proteins/api/proteomes/{upid}" +#' "GET https://ebi.ac.uk/proteins/api/proteomes/proteins/\{upid\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/proteomes/\{upid\}" #' #' @param upid \href{https://www.uniprot.org/help/proteome_id}{UniProt Proteome #' identifier (UPID)}. You can supply up to 100 UPIDs. @@ -397,7 +397,7 @@ rba_uniprot_genecentric_search <- function(upid = NULL, #' gene-centric isoform mapping for eukaryotic reference proteome entries.}. #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/genecentric/{accession}" +#' "GET https://ebi.ac.uk/proteins/api/genecentric/\{accession\}" #' #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ #' UniProtKB primary or secondary accession}. diff --git a/R/uniprot_taxonomy.R b/R/uniprot_taxonomy.R index d5435de5..44a9c1a4 100644 --- a/R/uniprot_taxonomy.R +++ b/R/uniprot_taxonomy.R @@ -7,7 +7,7 @@ #' \href{https://www.uniprot.org/help/taxonomy}{UniProt Taxonomy database} #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/ancestor/{ids}" +#' "GET https://ebi.ac.uk/proteins/api/ancestor/\{ids\}" #' #' @param ids (numeric) Numeric vector of #' \href{https://www.uniprot.org/help/taxonomic_identifier}{NCBI taxonomic @@ -75,15 +75,15 @@ rba_uniprot_taxonomy_lca <- function(ids, #' \href{https://www.uniprot.org/help/taxonomy}{UniProt Taxonomy database}. #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/ids/{ids}" -#' \cr "GET https://ebi.ac.uk/proteins/api/ids//id/{id}/node" -#' \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/node" -#' \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/children" -#' \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/children/node" -#' \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/parent" -#' \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/parent/node" -#' \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/siblings" -#' \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/siblings/node" +#' "GET https://ebi.ac.uk/proteins/api/ids/\{ids\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/ids/id/\{id\}/node" +#' \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/node" +#' \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/children" +#' \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/children/node" +#' \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/parent" +#' \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/parent/node" +#' \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/siblings" +#' \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/siblings/node" #' #' @param ids (numeric) a single or a numeric vector of #' \href{https://www.uniprot.org/help/taxonomic_identifier}{NCBI taxonomic @@ -207,8 +207,8 @@ rba_uniprot_taxonomy <- function(ids, #' taxonomy node. #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/lineage/{id}" -#' \cr "GET https://ebi.ac.uk/proteins/api/lineage/{id}" +#' "GET https://ebi.ac.uk/proteins/api/lineage/\{id\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/lineage/\{id\}" #' #' @param id (numeric) a #' \href{https://www.uniprot.org/help/taxonomic_identifier}{NCBI taxonomic @@ -273,8 +273,8 @@ rba_uniprot_taxonomy_lineage <- function(id, #' \href{https://www.uniprot.org/help/taxonomy}{UniProt Taxonomy database}. #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/name/{name}" -#' \cr "GET https://ebi.ac.uk/proteins/api/name/{name}/node" +#' "GET https://ebi.ac.uk/proteins/api/name/\{name\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/name/\{name\}/node" #' #' @param name a name to to be used as search query. #' @param field Specify the field that your supplied name should be searched. diff --git a/R/uniprot_uniparc.R b/R/uniprot_uniparc.R index 09940057..810bddd9 100644 --- a/R/uniprot_uniparc.R +++ b/R/uniprot_uniparc.R @@ -257,10 +257,10 @@ rba_uniprot_uniparc_search <- function(upi = NULL, #' the returned UniParc entry. see "Argument" section for more details. #' #' @section Corresponding API Resources: -#' "GET https://ebi.ac.uk/proteins/api/uniparc/accession/{accession} " -#' \cr "GET https://ebi.ac.uk/proteins/api/uniparc/dbreference/{dbid}" -#' \cr "GET https://ebi.ac.uk/proteins/api/uniparc/proteome/{upid}" -#' \cr "GET https://ebi.ac.uk/proteins/api/uniparc/upi/{upi}" +#' "GET https://ebi.ac.uk/proteins/api/uniparc/accession/\{accession\} " +#' \cr "GET https://ebi.ac.uk/proteins/api/uniparc/dbreference/\{dbid\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/uniparc/proteome/\{upid\}" +#' \cr "GET https://ebi.ac.uk/proteins/api/uniparc/upi/\{upi\}" #' #' @param upi unique UniParc Identifier. #' @param accession \href{https://www.uniprot.org/help/accession_numbers}{ diff --git a/man/rba_jaspar_collections.Rd b/man/rba_jaspar_collections.Rd index 645044f2..e3717e9c 100644 --- a/man/rba_jaspar_collections.Rd +++ b/man/rba_jaspar_collections.Rd @@ -23,7 +23,7 @@ JASPAR organizes matrix profiles into collections. } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/collections/" + "GET https://jaspar.elixir.no/api/v1/collections/" } \examples{ diff --git a/man/rba_jaspar_collections_matrices.Rd b/man/rba_jaspar_collections_matrices.Rd index 709f1c0a..05997ad1 100644 --- a/man/rba_jaspar_collections_matrices.Rd +++ b/man/rba_jaspar_collections_matrices.Rd @@ -60,7 +60,7 @@ The results are paginated. You can control the page's size number } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/collections/{collection}/" + "GET https://jaspar.elixir.no/api/v1/collections/\{collection\}/" } \examples{ diff --git a/man/rba_jaspar_matrix.Rd b/man/rba_jaspar_matrix.Rd index 8360b905..7efa53eb 100644 --- a/man/rba_jaspar_matrix.Rd +++ b/man/rba_jaspar_matrix.Rd @@ -35,7 +35,7 @@ Using this function you can retrieve a Position Frequency Matrices (PFM) } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/matrix/{matrix_id}/" + "GET https://jaspar.elixir.no/api/v1/matrix/\{matrix_id\}/" } \examples{ diff --git a/man/rba_jaspar_matrix_search.Rd b/man/rba_jaspar_matrix_search.Rd index 085070c1..9084ac57 100644 --- a/man/rba_jaspar_matrix_search.Rd +++ b/man/rba_jaspar_matrix_search.Rd @@ -83,7 +83,7 @@ Note that this is a search function. Thus, you are not required to fill } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/api/v1/matrix/" + "GET https://jaspar.elixir.no/api/v1/api/v1/matrix/" } \examples{ diff --git a/man/rba_jaspar_matrix_versions.Rd b/man/rba_jaspar_matrix_versions.Rd index d9b3710d..3238233f 100644 --- a/man/rba_jaspar_matrix_versions.Rd +++ b/man/rba_jaspar_matrix_versions.Rd @@ -29,7 +29,7 @@ Since JASPAR release 2010, the matrix profiles } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/matrix/{base_id}/versions/" + "GET https://jaspar.elixir.no/api/v1/matrix/\{base_id\}/versions/" } \examples{ diff --git a/man/rba_jaspar_releases.Rd b/man/rba_jaspar_releases.Rd index 6338e18b..ba4a58f4 100644 --- a/man/rba_jaspar_releases.Rd +++ b/man/rba_jaspar_releases.Rd @@ -25,8 +25,8 @@ If a release number was supplied, this function will return the details } \section{Corresponding API Resources}{ -"GET "https://jaspar.elixir.no/api/v1/releases/" - "GET "https://jaspar.elixir.no/api/v1/releases/{release_number}/" + "GET https://jaspar.elixir.no/api/v1/releases/" + \cr "GET https://jaspar.elixir.no/api/v1/releases/\{release_number\}/" } \examples{ diff --git a/man/rba_jaspar_sites.Rd b/man/rba_jaspar_sites.Rd index 0083c4ef..9d7cf63d 100644 --- a/man/rba_jaspar_sites.Rd +++ b/man/rba_jaspar_sites.Rd @@ -22,7 +22,7 @@ Use this function to retrieve a list of transcription factor binding sites } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/sites/{matrix_id}/" + "GET https://jaspar.elixir.no/api/v1/sites/\{matrix_id\}/" } \examples{ diff --git a/man/rba_jaspar_species.Rd b/man/rba_jaspar_species.Rd index 66a5b527..153aa6f2 100644 --- a/man/rba_jaspar_species.Rd +++ b/man/rba_jaspar_species.Rd @@ -30,7 +30,7 @@ JASPAR organizes matrix profiles from multiple species } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/species/" + "GET https://jaspar.elixir.no/api/v1/species/" } \examples{ diff --git a/man/rba_jaspar_species_matrices.Rd b/man/rba_jaspar_species_matrices.Rd index 5b08f18c..be2bc203 100644 --- a/man/rba_jaspar_species_matrices.Rd +++ b/man/rba_jaspar_species_matrices.Rd @@ -58,7 +58,7 @@ The results are paginated. You can control the page's size number } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/species/{tax_id}/" + "GET https://jaspar.elixir.no/api/v1/species/\{tax_id\}/" } \examples{ diff --git a/man/rba_jaspar_taxons.Rd b/man/rba_jaspar_taxons.Rd index 67f23152..e8a3ae1f 100644 --- a/man/rba_jaspar_taxons.Rd +++ b/man/rba_jaspar_taxons.Rd @@ -23,7 +23,7 @@ JASPAR organizes matrix profiles from multiple species } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/taxon/" + "GET https://jaspar.elixir.no/api/v1/taxon/" } \examples{ diff --git a/man/rba_jaspar_taxons_matrices.Rd b/man/rba_jaspar_taxons_matrices.Rd index a01cf8bc..31c819aa 100644 --- a/man/rba_jaspar_taxons_matrices.Rd +++ b/man/rba_jaspar_taxons_matrices.Rd @@ -60,7 +60,7 @@ The results are paginated. You can control the page's size number } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/taxon/{tax_group}/" + "GET https://jaspar.elixir.no/api/v1/taxon/\{tax_group\}/" } \examples{ diff --git a/man/rba_jaspar_tffm.Rd b/man/rba_jaspar_tffm.Rd index def0e2a4..d98a44ca 100644 --- a/man/rba_jaspar_tffm.Rd +++ b/man/rba_jaspar_tffm.Rd @@ -23,7 +23,7 @@ Using this function you can retrieve details and annotations of } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/fttm/{tffm_id}/" + "GET https://jaspar.elixir.no/api/v1/fttm/\{tffm_id\}/" } \examples{ diff --git a/man/rba_jaspar_tffm_search.Rd b/man/rba_jaspar_tffm_search.Rd index 84954370..cd6a8438 100644 --- a/man/rba_jaspar_tffm_search.Rd +++ b/man/rba_jaspar_tffm_search.Rd @@ -62,7 +62,7 @@ Note that this is a search function. Thus, you are not required to fill } \section{Corresponding API Resources}{ - "GET "https://jaspar.elixir.no/api/v1/api/v1/tffm/" + "GET https://jaspar.elixir.no/api/v1/api/v1/tffm/" } \examples{ diff --git a/man/rba_mieaa_cats.Rd b/man/rba_mieaa_cats.Rd index 13a71327..8a348061 100644 --- a/man/rba_mieaa_cats.Rd +++ b/man/rba_mieaa_cats.Rd @@ -37,7 +37,7 @@ For each Combination of species and miRNA type, Only a pre-defined } \section{Corresponding API Resources}{ - "GET "https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_categories/{species}/{mirna_type}/" + "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_categories/\{species\}/\{mirna_type\}/" } \examples{ diff --git a/man/rba_mieaa_enrich_results.Rd b/man/rba_mieaa_enrich_results.Rd index 8c7b02f0..67706a20 100644 --- a/man/rba_mieaa_enrich_results.Rd +++ b/man/rba_mieaa_enrich_results.Rd @@ -35,7 +35,7 @@ Note that using \code{\link{rba_mieaa_enrich}} is a more convenient way to } \section{Corresponding API Resources}{ - "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/results/{job_id}" + "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/results/\{job_id\}" } \examples{ diff --git a/man/rba_mieaa_enrich_status.Rd b/man/rba_mieaa_enrich_status.Rd index 0de2e915..ebcc038f 100644 --- a/man/rba_mieaa_enrich_status.Rd +++ b/man/rba_mieaa_enrich_status.Rd @@ -31,7 +31,7 @@ Note that using \code{\link{rba_mieaa_enrich}} is a more convenient way to } \section{Corresponding API Resources}{ - "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/job_status/{job_id}" + "GET https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/job_status/\{job_id\}" } \examples{ diff --git a/man/rba_mieaa_enrich_submit.Rd b/man/rba_mieaa_enrich_submit.Rd index 6cedea72..bc224fbc 100644 --- a/man/rba_mieaa_enrich_submit.Rd +++ b/man/rba_mieaa_enrich_submit.Rd @@ -97,7 +97,7 @@ Note that using \code{\link{rba_mieaa_enrich}} is a more convenient way to } \section{Corresponding API Resources}{ - "POST https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_analysis/{species}/{type}/{test}/" + "POST https://ccb-compute2.cs.uni-saarland.de/mieaa2/api/v1/enrichment_analysis/\{species\}/\{type\}/\{test\}/" } \examples{ diff --git a/man/rba_reactome_analysis_download.Rd b/man/rba_reactome_analysis_download.Rd index 6e24d4d9..66959504 100644 --- a/man/rba_reactome_analysis_download.Rd +++ b/man/rba_reactome_analysis_download.Rd @@ -60,14 +60,14 @@ Token is associated to each Reactome analysis results and kept by Reactome } \section{Corresponding API Resources}{ -GET https://reactome.org/AnalysisService/download/{token}/entities/ -found/{resource}/{filename}.csv" -GET https://reactome.org/AnalysisService//download/{token}/entities/ -notfound/{filename}.csv" -GET https://reactome.org/AnalysisService/download/{token}/pathways/ -{resource}/{filename}.csv" -GET https://reactome.org/AnalysisService/download/{token}/result.json" -GET https://reactome.org/AnalysisService/download/{token}/result.json.gz" +GET https://reactome.org/AnalysisService/download/\{token\}/entities/ +found/\{resource\}/\{filename\}.csv" +\cr GET https://reactome.org/AnalysisService/download/\{token\}/entities/ +notfound/\{filename\}.csv" +\cr GET https://reactome.org/AnalysisService/download/\{token\}/pathways/ +\{resource\}/\{filename\}.csv" +\cr GET https://reactome.org/AnalysisService/download/\{token\}/result.json" +\cr GET https://reactome.org/AnalysisService/download/\{token\}/result.json.gz" } \examples{ diff --git a/man/rba_reactome_analysis_pdf.Rd b/man/rba_reactome_analysis_pdf.Rd index 3cb77a18..bcfec14e 100644 --- a/man/rba_reactome_analysis_pdf.Rd +++ b/man/rba_reactome_analysis_pdf.Rd @@ -72,8 +72,8 @@ Token is associated to each Reactome analysis results and kept by Reactome } \section{Corresponding API Resources}{ - "GET https://reactome.org/AnalysisService/report/{token}/{species}/ - {filename}.pdf" + "GET https://reactome.org/AnalysisService/report/\{token\}/\{species\}/ + \{filename\}.pdf" } \examples{ diff --git a/man/rba_reactome_analysis_species.Rd b/man/rba_reactome_analysis_species.Rd index 6614d51d..1dd01715 100644 --- a/man/rba_reactome_analysis_species.Rd +++ b/man/rba_reactome_analysis_species.Rd @@ -66,7 +66,7 @@ Reactome incorporate manually curated human reactions and PANTHER's } \section{Corresponding API Resources}{ - "GET https://reactome.org/AnalysisService/species/homoSapiens/{species}" + "GET https://reactome.org/AnalysisService/species/homoSapiens/\{species\}" } \examples{ diff --git a/man/rba_reactome_analysis_token.Rd b/man/rba_reactome_analysis_token.Rd index c7e9dd03..45e58e7f 100644 --- a/man/rba_reactome_analysis_token.Rd +++ b/man/rba_reactome_analysis_token.Rd @@ -76,7 +76,7 @@ After Any Analysis, Reactome will associate a token to your analysis. It } \section{Corresponding API Resources}{ - "GET https://reactome.org/AnalysisService/token/{token}" + "GET https://reactome.org/AnalysisService/token/\{token\}" } \examples{ diff --git a/man/rba_reactome_complex_list.Rd b/man/rba_reactome_complex_list.Rd index 5050613e..8e4a042c 100644 --- a/man/rba_reactome_complex_list.Rd +++ b/man/rba_reactome_complex_list.Rd @@ -26,8 +26,8 @@ This function will retrieve a list of complexes that include your supplied } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/complexes/{resource}/ - {identifier}" + "GET https://reactome.org/ContentService/data/complexes/\{resource\}/ + \{identifier\}" } \examples{ diff --git a/man/rba_reactome_complex_subunits.Rd b/man/rba_reactome_complex_subunits.Rd index 9df53ca1..7130a753 100644 --- a/man/rba_reactome_complex_subunits.Rd +++ b/man/rba_reactome_complex_subunits.Rd @@ -30,7 +30,7 @@ Subunits will be returned recursively; Which means that if a subunit was } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/complex/{id}/subunits" + "GET https://reactome.org/ContentService/data/complex/\{id\}/subunits" } \examples{ diff --git a/man/rba_reactome_diseases.Rd b/man/rba_reactome_diseases.Rd index 86cce6ed..2a9c9b56 100644 --- a/man/rba_reactome_diseases.Rd +++ b/man/rba_reactome_diseases.Rd @@ -23,8 +23,8 @@ This function Retrieve a list of all diseases or disease DOIDs annotated in } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/GET data/diseases" - "GET https://reactome.org/ContentService/GET data/diseases/doid" + "GET https://reactome.org/ContentService/data/diseases" + \cr "GET https://reactome.org/ContentService/data/diseases/doid" } \examples{ diff --git a/man/rba_reactome_entity_other_forms.Rd b/man/rba_reactome_entity_other_forms.Rd index 438602c4..cf5c89de 100644 --- a/man/rba_reactome_entity_other_forms.Rd +++ b/man/rba_reactome_entity_other_forms.Rd @@ -27,7 +27,7 @@ According to Reactome API documentation, "These other forms are Physical } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/entity/{id}/otherForms" + "GET https://reactome.org/ContentService/data/entity/\{id\}/otherForms" } \examples{ diff --git a/man/rba_reactome_event_ancestors.Rd b/man/rba_reactome_event_ancestors.Rd index 516e4222..71573910 100644 --- a/man/rba_reactome_event_ancestors.Rd +++ b/man/rba_reactome_event_ancestors.Rd @@ -33,7 +33,7 @@ By Reactome's definition, Events are the building blocks of biological } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/event/{id}/ancestors" + "GET https://reactome.org/ContentService/data/event/\{id\}/ancestors" } \examples{ diff --git a/man/rba_reactome_event_hierarchy.Rd b/man/rba_reactome_event_hierarchy.Rd index 3f864381..db4b926e 100644 --- a/man/rba_reactome_event_hierarchy.Rd +++ b/man/rba_reactome_event_hierarchy.Rd @@ -36,7 +36,7 @@ By Reactome's definition, Events are the building blocks of biological } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/eventsHierarchy/{species}" + "GET https://reactome.org/ContentService/data/eventsHierarchy/\{species\}" } \examples{ diff --git a/man/rba_reactome_exporter_diagram.Rd b/man/rba_reactome_exporter_diagram.Rd index 2e6724bd..7eb3f28b 100644 --- a/man/rba_reactome_exporter_diagram.Rd +++ b/man/rba_reactome_exporter_diagram.Rd @@ -114,10 +114,10 @@ If the function is called with create_document = FALSE: } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/exporter/diagram/{identifier} - .{ext}" - "GET https://reactome.org/ContentService/exporter/document/event/ - {identifier}.pdf" + "GET https://reactome.org/ContentService/exporter/diagram/\{identifier\} + .\{ext\}" + \cr "GET https://reactome.org/ContentService/exporter/document/event/ + \{identifier\}.pdf" } \examples{ diff --git a/man/rba_reactome_exporter_event.Rd b/man/rba_reactome_exporter_event.Rd index ad59f337..69528746 100644 --- a/man/rba_reactome_exporter_event.Rd +++ b/man/rba_reactome_exporter_event.Rd @@ -29,10 +29,10 @@ This function will export a supplied Reactome Event (Pathway or Reaction) } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService//exporter/event/ - {identifier}.sbgn" - "GET https://reactome.org/ContentService//exporter/event/ - {identifier}.sbml" + "GET https://reactome.org/ContentService/exporter/event/ + \{identifier\}.sbgn" + \cr "GET https://reactome.org/ContentService/exporter/event/ + \{identifier\}.sbml" } \examples{ diff --git a/man/rba_reactome_exporter_overview.Rd b/man/rba_reactome_exporter_overview.Rd index f976179c..79a013dd 100644 --- a/man/rba_reactome_exporter_overview.Rd +++ b/man/rba_reactome_exporter_overview.Rd @@ -81,7 +81,7 @@ This function will Save a Pathway Overview of the supplied specie } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/exporter/fireworks/{species}.{ext}" + "GET https://reactome.org/ContentService/exporter/fireworks/\{species\}.\{ext\}" } \examples{ diff --git a/man/rba_reactome_exporter_reaction.Rd b/man/rba_reactome_exporter_reaction.Rd index 437aeddc..03b01889 100644 --- a/man/rba_reactome_exporter_reaction.Rd +++ b/man/rba_reactome_exporter_reaction.Rd @@ -84,8 +84,8 @@ Note that this function will save Reaction-like event separately and out } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService//exporter/reaction/ - {identifier}.{ext}" + "GET https://reactome.org/ContentService/exporter/reaction/ + \{identifier\}.\{ext\}" } \examples{ diff --git a/man/rba_reactome_interactors_psicquic.Rd b/man/rba_reactome_interactors_psicquic.Rd index bbc07bd3..7451733a 100644 --- a/man/rba_reactome_interactors_psicquic.Rd +++ b/man/rba_reactome_interactors_psicquic.Rd @@ -41,10 +41,10 @@ You can call this function in two scenarios: \section{Corresponding API Resources}{ "POST https://reactome.org/ContentService/interactors/psicquic/molecules/ - {resource}/details" - "POST https://reactome.org/ContentService/interactors/psicquic/molecules/ - {resource}/summary" - "GET https://reactome.org/ContentService/interactors/psicquic/resources" + \{resource\}/details" + \cr "POST https://reactome.org/ContentService/interactors/psicquic/molecules/ + \{resource\}/summary" + \cr "GET https://reactome.org/ContentService/interactors/psicquic/resources" } \examples{ diff --git a/man/rba_reactome_mapping.Rd b/man/rba_reactome_mapping.Rd index 30108059..57bf7eb7 100644 --- a/man/rba_reactome_mapping.Rd +++ b/man/rba_reactome_mapping.Rd @@ -35,10 +35,10 @@ By providing an external identifier from a given resource, you can retrieve } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/mapping/{resource}/ - {identifier}/pathways" - \cr "GET https://reactome.org/ContentService/data/mapping/{resource}/ - {identifier}/reactions" + "GET https://reactome.org/ContentService/data/mapping/\{resource\}/ + \{identifier\}/pathways" + \cr "GET https://reactome.org/ContentService/data/mapping/\{resource\}/ + \{identifier\}/reactions" } \examples{ diff --git a/man/rba_reactome_orthology.Rd b/man/rba_reactome_orthology.Rd index 9da978b9..53e35cd7 100644 --- a/man/rba_reactome_orthology.Rd +++ b/man/rba_reactome_orthology.Rd @@ -38,7 +38,7 @@ In version 73 (11 June 2020), using an orthology-based approach, \section{Corresponding API Resources}{ "POST https://reactome.org/ContentService/data/orthologies/ids/ - species/{speciesId}" + species/\{speciesId\}" } \examples{ diff --git a/man/rba_reactome_participant_of.Rd b/man/rba_reactome_participant_of.Rd index 7076ecb7..938c12f3 100644 --- a/man/rba_reactome_participant_of.Rd +++ b/man/rba_reactome_participant_of.Rd @@ -23,7 +23,7 @@ This function will retrieve a list of complexes and sets that Your } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/entity/{id}/componentOf" + "GET https://reactome.org/ContentService/data/entity/\{id\}/componentOf" } \examples{ diff --git a/man/rba_reactome_participants.Rd b/man/rba_reactome_participants.Rd index 8a8e5da1..181c0fbc 100644 --- a/man/rba_reactome_participants.Rd +++ b/man/rba_reactome_participants.Rd @@ -56,10 +56,10 @@ A 'Physical Entity' Instance could include an individual molecule, } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/participants/{id}" - \cr "GET https://reactome.org/ContentService/data/participants/{id}/ + "GET https://reactome.org/ContentService/data/participants/\{id\}" + \cr "GET https://reactome.org/ContentService/data/participants/\{id\}/ participatingPhysicalEntities" - \cr "GET https://reactome.org/ContentService/data/participants/{id}/ + \cr "GET https://reactome.org/ContentService/data/participants/\{id\}/ referenceEntities" } diff --git a/man/rba_reactome_pathways_events.Rd b/man/rba_reactome_pathways_events.Rd index e8f33784..51c2af7a 100644 --- a/man/rba_reactome_pathways_events.Rd +++ b/man/rba_reactome_pathways_events.Rd @@ -37,10 +37,10 @@ By Reactome's definition, Events are the building blocks of biological } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/pathway/{id}/ + "GET https://reactome.org/ContentService/data/pathway/\{id\}/ containedEvents" - \cr "GET https://reactome.org/ContentService/data/pathway/{id}/ - containedEvents/{attributeName}" + \cr "GET https://reactome.org/ContentService/data/pathway/\{id\}/ + containedEvents/\{attributeName\}" } \examples{ diff --git a/man/rba_reactome_pathways_low.Rd b/man/rba_reactome_pathways_low.Rd index 90613121..536376cd 100644 --- a/man/rba_reactome_pathways_low.Rd +++ b/man/rba_reactome_pathways_low.Rd @@ -44,11 +44,11 @@ Use this function to search the event hierarchy and retrieve a list of } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/pathways/low/entity/{id}" + "GET https://reactome.org/ContentService/data/pathways/low/entity/\{id\}" \cr "GET https://reactome.org/ContentService/data/pathways/low/diagram/ - entity/{id}" + entity/\{id\}" \cr "GET https://reactome.org/ContentService/data/pathways/low/diagram/ - entity/{id}/allForms" + entity/\{id\}/allForms" } \examples{ diff --git a/man/rba_reactome_pathways_top.Rd b/man/rba_reactome_pathways_top.Rd index 3b7c3580..a374eb5b 100644 --- a/man/rba_reactome_pathways_top.Rd +++ b/man/rba_reactome_pathways_top.Rd @@ -34,7 +34,7 @@ Reactome's Events hierarchy for any specie will begin with pathways with } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/pathways/top/{species}" + "GET https://reactome.org/ContentService/data/pathways/top/\{species\}" } \examples{ diff --git a/man/rba_reactome_people_name.Rd b/man/rba_reactome_people_name.Rd index 87a61600..0b575ec3 100644 --- a/man/rba_reactome_people_name.Rd +++ b/man/rba_reactome_people_name.Rd @@ -25,8 +25,8 @@ Using this function you can query people by partially matching or exact } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/data/people/name/{name}" - \cr "GET https://reactome.org/ContentService/data/people/name/{name}/exact" + "GET https://reactome.org/ContentService/data/people/name/\{name\}" + \cr "GET https://reactome.org/ContentService/data/people/name/\{name\}/exact" } \examples{ diff --git a/man/rba_reactome_query.Rd b/man/rba_reactome_query.Rd index f02f9920..f1bbb400 100644 --- a/man/rba_reactome_query.Rd +++ b/man/rba_reactome_query.Rd @@ -43,9 +43,9 @@ Using this Comprehensive function, You can Retrieve any object from "POST https://reactome.org/ContentService/data/query/ids" \cr "POST https://reactome.org/ContentService/data/query/ids/map" - \cr "GET https://reactome.org/ContentService/data/query/{id}" - \cr s"GET https://reactome.org/ContentService//data/query/enhanced/{id}" - \cr "GET https://reactome.org/ContentService/data/query/{id}/{attributeName}" + \cr "GET https://reactome.org/ContentService/data/query/\{id\}" + \cr "GET https://reactome.org/ContentService/data/query/enhanced/\{id\}" + \cr "GET https://reactome.org/ContentService/data/query/\{id\}/\{attributeName\}" } \examples{ diff --git a/man/rba_reactome_xref.Rd b/man/rba_reactome_xref.Rd index 593148bf..e108511d 100644 --- a/man/rba_reactome_xref.Rd +++ b/man/rba_reactome_xref.Rd @@ -31,7 +31,7 @@ Reactome cross-references external database's identifiers to it's database } \section{Corresponding API Resources}{ - "GET https://reactome.org/ContentService/references/mapping/{identifier}" + "GET https://reactome.org/ContentService/references/mapping/\{identifier\}" } \examples{ diff --git a/man/rba_string_annotations.Rd b/man/rba_string_annotations.Rd index e96eb9ab..26b2bc73 100644 --- a/man/rba_string_annotations.Rd +++ b/man/rba_string_annotations.Rd @@ -53,8 +53,8 @@ STRING currently maps to and retrieve enrichment results based on Gene } \section{Corresponding API Resources}{ - "POST https://string-db.org/api/[output_format]/functional_annotation? - identifiers=[your_identifiers]&[optional_parameters]" + "POST https://string-db.org/api/\{output_format\}/functional_annotation? + identifiers=\{your_identifiers\}&\{optional_parameters\}" } \examples{ diff --git a/man/rba_string_enrichment.Rd b/man/rba_string_enrichment.Rd index 53a75716..d359300c 100644 --- a/man/rba_string_enrichment.Rd +++ b/man/rba_string_enrichment.Rd @@ -54,8 +54,8 @@ STRING currently maps to and retrieve enrichment results based on Gene } \section{Corresponding API Resources}{ - "POST https://string-db.org/api/[output_format]/enrichment?identifiers= - [your_identifiers]&[optional_parameters]" + "POST https://string-db.org/api/\{output_format\}/enrichment?identifiers= + \{your_identifiers\}&\{optional_parameters\}" } \examples{ diff --git a/man/rba_string_enrichment_ppi.Rd b/man/rba_string_enrichment_ppi.Rd index 981b9403..3577f92b 100644 --- a/man/rba_string_enrichment_ppi.Rd +++ b/man/rba_string_enrichment_ppi.Rd @@ -42,8 +42,8 @@ Even when there is no annotation for your input proteins, STRING can Compare } \section{Corresponding API Resources}{ - "POST https://string-db.org/api/[output_format]/ppi_enrichment?identifiers= - [your_identifiers]&[optional_parameters]" + "POST https://string-db.org/api/\{output_format\}/ppi_enrichment?identifiers= + \{your_identifiers\}&\{optional_parameters\}" } \examples{ diff --git a/man/rba_string_homology_inter.Rd b/man/rba_string_homology_inter.Rd index 1266d579..c8a7e229 100644 --- a/man/rba_string_homology_inter.Rd +++ b/man/rba_string_homology_inter.Rd @@ -43,8 +43,8 @@ Note that this function will return the highest similarity score hits of } \section{Corresponding API Resources}{ - "POST https://string-db.org/api/[output-format]/homology_best? - identifiers=[your_identifiers]" + "POST https://string-db.org/api/\{output-format\}/homology_best? + identifiers=\{your_identifiers\}" } \examples{ diff --git a/man/rba_string_homology_intra.Rd b/man/rba_string_homology_intra.Rd index b69841f4..d587a74c 100644 --- a/man/rba_string_homology_intra.Rd +++ b/man/rba_string_homology_intra.Rd @@ -39,8 +39,8 @@ Note that this function will retrieve similarity scores of different } \section{Corresponding API Resources}{ - "POST https://string-db.org/api/[output-format]/homology?identifiers= - [your_identifiers]" + "POST https://string-db.org/api/\{output-format\}/homology?identifiers= + \{your_identifiers\}" } \examples{ diff --git a/man/rba_string_interaction_partners.Rd b/man/rba_string_interaction_partners.Rd index 73c38ca8..1b1ebcbd 100644 --- a/man/rba_string_interaction_partners.Rd +++ b/man/rba_string_interaction_partners.Rd @@ -56,8 +56,8 @@ Note that this function will retrieve the interactions between your input } \section{Corresponding API Resources}{ - "POST https://string-db.org/api/[output-format]/ - interaction_partners?identifiers=[your_identifiers]&[optional_parameters]" + "POST https://string-db.org/api/\{output-format\}/ + interaction_partners?identifiers=\{your_identifiers\}&\{optional_parameters\}" } \examples{ diff --git a/man/rba_string_interactions_network.Rd b/man/rba_string_interactions_network.Rd index 2389c0b7..df7448d8 100644 --- a/man/rba_string_interactions_network.Rd +++ b/man/rba_string_interactions_network.Rd @@ -79,8 +79,8 @@ Note that this function will return interactions between your set of } \section{Corresponding API Resources}{ - "POST https://string-db.org/api/[output-format]/network?identifiers= - [your_identifiers]&[optional_parameters]" + "POST https://string-db.org/api/\{output-format\}/network?identifiers= + \{your_identifiers\}&\{optional_parameters\}" } \examples{ diff --git a/man/rba_string_map_ids.Rd b/man/rba_string_map_ids.Rd index 8d7c4b6e..091191d1 100644 --- a/man/rba_string_map_ids.Rd +++ b/man/rba_string_map_ids.Rd @@ -34,8 +34,8 @@ This function Calls STRING's API to Convert a set of identifiers } \section{Corresponding API Resources}{ - "POST https://string-db.org/api/[output-format]/get_string_ids?identifiers= - [your_identifiers]&[optional_parameters]" + "POST https://string-db.org/api/\{output-format\}/get_string_ids?identifiers= + \{your_identifiers\}&\{optional_parameters\}" } \examples{ diff --git a/man/rba_string_network_image.Rd b/man/rba_string_network_image.Rd index da5395f8..64e12328 100644 --- a/man/rba_string_network_image.Rd +++ b/man/rba_string_network_image.Rd @@ -104,8 +104,8 @@ Depending on that you supplied a single protein ID or more than one protein } \section{Corresponding API Resources}{ - "POST https://string-db.org/api/[output-format]/network?identifiers= - [your_identifiers]&[optional_parameters]" + "POST https://string-db.org/api/\{output-format\}/network?identifiers= + \{your_identifiers\}&\{optional_parameters\}" } \examples{ diff --git a/man/rba_string_version.Rd b/man/rba_string_version.Rd index a3c7632f..0798e708 100644 --- a/man/rba_string_version.Rd +++ b/man/rba_string_version.Rd @@ -25,7 +25,7 @@ Note that STRING releases new version at approximately 2 years cycle. } \section{Corresponding API Resources}{ - "GET https://string-db.org/api/[output_format]/version" + "GET https://string-db.org/api/\{output_format\}/version" } \examples{ diff --git a/man/rba_uniprot_antigens.Rd b/man/rba_uniprot_antigens.Rd index 012705f8..42147534 100644 --- a/man/rba_uniprot_antigens.Rd +++ b/man/rba_uniprot_antigens.Rd @@ -24,7 +24,7 @@ UniProt maps Antigenic features from different sources to the proteins' } \section{Corresponding API Resources}{ - "GET https://www.ebi.ac.uk/proteins/api/antigen/{accession}" + "GET https://www.ebi.ac.uk/proteins/api/antigen/\{accession\}" } \examples{ diff --git a/man/rba_uniprot_coordinates.Rd b/man/rba_uniprot_coordinates.Rd index 4e2ffe62..c4c78200 100644 --- a/man/rba_uniprot_coordinates.Rd +++ b/man/rba_uniprot_coordinates.Rd @@ -37,8 +37,8 @@ For more information about how UniProt imports and calculates genomic } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/coordinates/{accession}" - \cr "GET https://ebi.ac.uk/proteins/api/coordinates/{dbtype}:{dbid}" + "GET https://ebi.ac.uk/proteins/api/coordinates/\{accession\}" + \cr "GET https://ebi.ac.uk/proteins/api/coordinates/\{dbtype\}:\{dbid\}" } \examples{ diff --git a/man/rba_uniprot_coordinates_location.Rd b/man/rba_uniprot_coordinates_location.Rd index 1026a33c..3457c818 100644 --- a/man/rba_uniprot_coordinates_location.Rd +++ b/man/rba_uniprot_coordinates_location.Rd @@ -40,8 +40,10 @@ For more information about how UniProt imports and calculates genomic } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/coordinates/{taxonomy}/{locations}/feature" - \cr "GET https://ebi.ac.uk/proteins/api/coordinates/{taxonomy}/{locations}" + "GET https://ebi.ac.uk/proteins/api/coordinates + /\{taxonomy\}/\{locations\}/feature" + \cr "GET https://ebi.ac.uk/proteins/api/coordinates + /\{taxonomy\}/\{locations\}" } \examples{ diff --git a/man/rba_uniprot_coordinates_sequence.Rd b/man/rba_uniprot_coordinates_sequence.Rd index 06d78150..0903da8e 100644 --- a/man/rba_uniprot_coordinates_sequence.Rd +++ b/man/rba_uniprot_coordinates_sequence.Rd @@ -43,8 +43,10 @@ For more information about how UniProt imports and calculates genomic } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/coordinates/location/{accession}:{pPosition}" - \cr "GET https://ebi.ac.uk/proteins/api/coordinates/location/{accession}:{pStart}-{pEnd}" + "GET https://ebi.ac.uk/proteins/api/coordinates/location + /\{accession\}:\{pPosition\}" + \cr "GET https://ebi.ac.uk/proteins/api/coordinates/location + /\{accession\}:\{pStart\}-\{pEnd\}" } \examples{ diff --git a/man/rba_uniprot_features.Rd b/man/rba_uniprot_features.Rd index d4e57349..aba23d28 100644 --- a/man/rba_uniprot_features.Rd +++ b/man/rba_uniprot_features.Rd @@ -40,7 +40,7 @@ Use this function to retrieve } \section{Corresponding API Resources}{ - "GET https://www.ebi.ac.uk/proteins/api/features/{accession}" + "GET https://www.ebi.ac.uk/proteins/api/features/\{accession\}" } \examples{ diff --git a/man/rba_uniprot_genecentric.Rd b/man/rba_uniprot_genecentric.Rd index cb2ad321..9553cc70 100644 --- a/man/rba_uniprot_genecentric.Rd +++ b/man/rba_uniprot_genecentric.Rd @@ -25,7 +25,7 @@ Using this function you can retrieve gene-centrics data. For more } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/genecentric/{accession}" + "GET https://ebi.ac.uk/proteins/api/genecentric/\{accession\}" } \examples{ diff --git a/man/rba_uniprot_mutagenesis.Rd b/man/rba_uniprot_mutagenesis.Rd index 5caa693d..936bfef3 100644 --- a/man/rba_uniprot_mutagenesis.Rd +++ b/man/rba_uniprot_mutagenesis.Rd @@ -29,7 +29,7 @@ UniProt describes the effects of mutations in proteins' amino acid } \section{Corresponding API Resources}{ - "GET https://www.ebi.ac.uk/proteins/api/mutagenesis/{accession}" + "GET https://www.ebi.ac.uk/proteins/api/mutagenesis/\{accession\}" } \examples{ diff --git a/man/rba_uniprot_proteins.Rd b/man/rba_uniprot_proteins.Rd index 6b3053c7..c472e8a7 100644 --- a/man/rba_uniprot_proteins.Rd +++ b/man/rba_uniprot_proteins.Rd @@ -34,9 +34,9 @@ Use this function to retrieve a UniProt Entry by it's UniProt accession. } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/proteins/{accession}" - \cr "GET https://ebi.ac.uk/proteins/api/proteins/interaction/{accession}" - \cr "GET https://ebi.ac.uk/proteins/api/proteins/{accession}/isoforms" + "GET https://ebi.ac.uk/proteins/api/proteins/\{accession\}" + \cr "GET https://ebi.ac.uk/proteins/api/proteins/interaction/\{accession\}" + \cr "GET https://ebi.ac.uk/proteins/api/proteins/\{accession\}/isoforms" } \examples{ diff --git a/man/rba_uniprot_proteins_crossref.Rd b/man/rba_uniprot_proteins_crossref.Rd index 553313f8..e356966a 100644 --- a/man/rba_uniprot_proteins_crossref.Rd +++ b/man/rba_uniprot_proteins_crossref.Rd @@ -43,7 +43,7 @@ List which each element is a UniProt entity that correspond to } \section{Corresponding API Resources}{ - "GET https://www.ebi.ac.uk/proteins/api/proteins/{dbtype}:{dbid}" + "GET https://www.ebi.ac.uk/proteins/api/proteins/\{dbtype\}:\{dbid\}" } \examples{ diff --git a/man/rba_uniprot_proteomes.Rd b/man/rba_uniprot_proteomes.Rd index d54b4c9b..8cebdc82 100644 --- a/man/rba_uniprot_proteomes.Rd +++ b/man/rba_uniprot_proteomes.Rd @@ -35,8 +35,8 @@ UniProt collects and annotates proteomes(Protein sets expressed in an } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/proteomes/proteins/{upid}" - \cr "GET https://ebi.ac.uk/proteins/api/proteomes/{upid}" + "GET https://ebi.ac.uk/proteins/api/proteomes/proteins/\{upid\}" + \cr "GET https://ebi.ac.uk/proteins/api/proteomes/\{upid\}" } \examples{ diff --git a/man/rba_uniprot_proteomics.Rd b/man/rba_uniprot_proteomics.Rd index 822fb9e7..1b013fcf 100644 --- a/man/rba_uniprot_proteomics.Rd +++ b/man/rba_uniprot_proteomics.Rd @@ -24,7 +24,7 @@ UniProt maps proteomics peptides from different sources to the proteins' } \section{Corresponding API Resources}{ - "GET https://www.ebi.ac.uk/proteins/api/proteomics/{accession}" + "GET https://www.ebi.ac.uk/proteins/api/proteomics/\{accession\}" } \examples{ diff --git a/man/rba_uniprot_ptm.Rd b/man/rba_uniprot_ptm.Rd index e371a04f..b614ab11 100644 --- a/man/rba_uniprot_ptm.Rd +++ b/man/rba_uniprot_ptm.Rd @@ -30,7 +30,7 @@ see also: } \section{Corresponding API Resources}{ - "GET https://www.ebi.ac.uk/proteins/api/proteomics-ptm/{accession}" + "GET https://www.ebi.ac.uk/proteins/api/proteomics-ptm/\{accession\}" } \examples{ diff --git a/man/rba_uniprot_taxonomy.Rd b/man/rba_uniprot_taxonomy.Rd index 46a32e05..571d1964 100644 --- a/man/rba_uniprot_taxonomy.Rd +++ b/man/rba_uniprot_taxonomy.Rd @@ -50,15 +50,15 @@ providing their } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/ids/{ids}" - \cr "GET https://ebi.ac.uk/proteins/api/ids//id/{id}/node" - \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/node" - \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/children" - \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/children/node" - \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/parent" - \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/parent/node" - \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/siblings" - \cr "GET https://ebi.ac.uk/proteins/api/id/{id}/siblings/node" + "GET https://ebi.ac.uk/proteins/api/ids/\{ids\}" + \cr "GET https://ebi.ac.uk/proteins/api/ids/id/\{id\}/node" + \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/node" + \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/children" + \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/children/node" + \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/parent" + \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/parent/node" + \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/siblings" + \cr "GET https://ebi.ac.uk/proteins/api/id/\{id\}/siblings/node" } \examples{ diff --git a/man/rba_uniprot_taxonomy_lca.Rd b/man/rba_uniprot_taxonomy_lca.Rd index 66f2e250..cd86a741 100644 --- a/man/rba_uniprot_taxonomy_lca.Rd +++ b/man/rba_uniprot_taxonomy_lca.Rd @@ -25,7 +25,7 @@ Use this function to retrieve lowest common ancestor (LCA) of two } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/ancestor/{ids}" + "GET https://ebi.ac.uk/proteins/api/ancestor/\{ids\}" } \examples{ diff --git a/man/rba_uniprot_taxonomy_lineage.Rd b/man/rba_uniprot_taxonomy_lineage.Rd index 0273052d..4efe1e3e 100644 --- a/man/rba_uniprot_taxonomy_lineage.Rd +++ b/man/rba_uniprot_taxonomy_lineage.Rd @@ -25,8 +25,8 @@ Use this function to retrieve the taxonomic lineage of your supplied } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/lineage/{id}" - \cr "GET https://ebi.ac.uk/proteins/api/lineage/{id}" + "GET https://ebi.ac.uk/proteins/api/lineage/\{id\}" + \cr "GET https://ebi.ac.uk/proteins/api/lineage/\{id\}" } \examples{ diff --git a/man/rba_uniprot_taxonomy_name.Rd b/man/rba_uniprot_taxonomy_name.Rd index 179f1154..4245e159 100644 --- a/man/rba_uniprot_taxonomy_name.Rd +++ b/man/rba_uniprot_taxonomy_name.Rd @@ -48,8 +48,8 @@ Using this function, you can search and retrieve taxonomic nodes using } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/name/{name}" - \cr "GET https://ebi.ac.uk/proteins/api/name/{name}/node" + "GET https://ebi.ac.uk/proteins/api/name/\{name\}" + \cr "GET https://ebi.ac.uk/proteins/api/name/\{name\}/node" } \examples{ diff --git a/man/rba_uniprot_uniparc.Rd b/man/rba_uniprot_uniparc.Rd index 9acf7d65..493bf241 100644 --- a/man/rba_uniprot_uniparc.Rd +++ b/man/rba_uniprot_uniparc.Rd @@ -59,10 +59,10 @@ Use this function to retrieve UniParc entries. You can use either -and only } \section{Corresponding API Resources}{ - "GET https://ebi.ac.uk/proteins/api/uniparc/accession/{accession} " - \cr "GET https://ebi.ac.uk/proteins/api/uniparc/dbreference/{dbid}" - \cr "GET https://ebi.ac.uk/proteins/api/uniparc/proteome/{upid}" - \cr "GET https://ebi.ac.uk/proteins/api/uniparc/upi/{upi}" + "GET https://ebi.ac.uk/proteins/api/uniparc/accession/\{accession\} " + \cr "GET https://ebi.ac.uk/proteins/api/uniparc/dbreference/\{dbid\}" + \cr "GET https://ebi.ac.uk/proteins/api/uniparc/proteome/\{upid\}" + \cr "GET https://ebi.ac.uk/proteins/api/uniparc/upi/\{upi\}" } \examples{ diff --git a/man/rba_uniprot_variation.Rd b/man/rba_uniprot_variation.Rd index 1b3b5c6f..dfcea73e 100644 --- a/man/rba_uniprot_variation.Rd +++ b/man/rba_uniprot_variation.Rd @@ -63,9 +63,9 @@ Retrieve natural variant annotations of a sequence using UniProt protein } \section{Corresponding API Resources}{ - "GET https://www.ebi.ac.uk/proteins/api/variation/dbsnp/{dbid}" - \cr "GET https://www.ebi.ac.uk/proteins/api/variation/hgvs/{hgvs}" - \cr "GET https://www.ebi.ac.uk/proteins/api/variation/{accession}" + "GET https://www.ebi.ac.uk/proteins/api/variation/dbsnp/\{dbid\}" + \cr "GET https://www.ebi.ac.uk/proteins/api/variation/hgvs/\{hgvs\}" + \cr "GET https://www.ebi.ac.uk/proteins/api/variation/\{accession\}" } \examples{