Man pages for ramiromagno/gwasrapidd
'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog
| add_object_tier | Adds an element named <obj_type> to content sub-element. |
| allele_name | Extract allele names from strings of the form rs123-G |
| ancestral_groups_tbl | Creates an ancestral groups table. |
| ancestries_tbl | Creates an ancestries table. |
| associations | Constructor for the S4 associations object. |
| associations-class | An S4 class to represent a set of GWAS Catalog associations |
| associations_drop_na | Drop any NA associations. |
| associations_tbl | Creates an associations table. |
| association_to_study | Map an association id to a study id |
| association_to_trait | Map an association id to an EFO trait id |
| association_to_variant | Map an association id to a variant id |
| bind | Bind GWAS Catalog objects |
| child_efo_ids | Get all child terms of this trait in the EFO hierarchy |
| contains_question_mark | Does a string contain a question mark? |
| countries_tbl | Creates a countries table. |
| cytogenetic_bands | GRCh38 human cytogenetic bands. |
| cytogenetic_band_to_genomic_range | Convert a cytogenetic band string to genomic coordinates. |
| empty_to_na | Converts an empty vector to a scalar NA |
| ensembl_ids_tbl | Creates an Ensembl gene identifiers' table. |
| entrez_ids_tbl | Creates an Entrez gene identifiers' table. |
| equal_length | Grows vectors to match longest vector |
| exists_variant | Check if a variant exists in the Catalog. |
| extract_association_id | Extract association identifiers from URLs |
| filter_by_id | Filter GWAS Catalog objects by identifier. |
| filter_variants_by_standard_chromosomes | Filter variants by standard human chromosomes. |
| gc_examples | gwasrapidd entities' examples |
| gc_get | Get a GWAS Catalog resource |
| gc_request | Request a GWAS Catalog REST API endpoint |
| gc_request_all | Request a paginated GWAS Catalog REST API endpoint |
| genomic_contexts_tbl | Creates a genomic contexts table. |
| genotyping_techs_tbl | Creates a genotyping technologies table. |
| get_associations | Get GWAS Catalog associations |
| get_associations_all | Get all GWAS Catalog associations |
| get_associations_by_association_id | Get GWAS Catalog associations by their association... |
| get_associations_by_efo_id | Get GWAS Catalog associations by EFO identifier |
| get_associations_by_efo_trait | Get GWAS Catalog associations by EFO traits |
| get_associations_by_pubmed_id | Get GWAS Catalog associations by PubMed identifiers |
| get_associations_by_study_id | Get GWAS Catalog associations by study identifiers |
| get_associations_by_variant_id | Get GWAS Catalog associations by variant identifiers |
| get_child_efo | Get all child terms of this trait in the EFO hierarchy |
| get_metadata | Get GWAS Catalog metadata |
| get_studies | Get GWAS Catalog studies |
| get_studies_all | Get all GWAS Catalog studies |
| get_studies_by_association_id | Get GWAS Catalog studies by association identifiers |
| get_studies_by_efo_id | Get GWAS Catalog studies by EFO identifier |
| get_studies_by_efo_trait | Get GWAS Catalog studies by EFO traits |
| get_studies_by_efo_uri | Get GWAS Catalog studies by EFO URIs |
| get_studies_by_full_pvalue_set | Get GWAS Catalog studies by full summary statistics criterion |
| get_studies_by_pubmed_id | Get GWAS Catalog studies by PubMed identifiers |
| get_studies_by_reported_trait | Get GWAS Catalog studies by reported traits |
| get_studies_by_study_id | Get GWAS Catalog studies by study identifiers |
| get_studies_by_user_requested | Get GWAS Catalog studies that have been requested by users or... |
| get_studies_by_variant_id | Get GWAS Catalog studies by variant identifiers |
| get_traits | Get GWAS Catalog EFO traits |
| get_traits_all | Get all GWAS Catalog EFO traits |
| get_traits_by_association_id | Get GWAS Catalog traits by association identifiers |
| get_traits_by_efo_id | Get GWAS Catalog traits by EFO identifier |
| get_traits_by_efo_trait | Get GWAS Catalog traits by EFO traits |
| get_traits_by_efo_uri | Get GWAS Catalog traits by EFO URIs |
| get_traits_by_pubmed_id | Get GWAS Catalog traits by PubMed identifiers |
| get_traits_by_study_id | Get GWAS Catalog traits by study identifiers |
| get_variants | Get GWAS Catalog variants |
| get_variants_all | Get all GWAS Catalog variants |
| get_variants_by_association_id | Get GWAS Catalog variants by their association identifiers |
| get_variants_by_cytogenetic_band | Get GWAS Catalog variants by cytogenetic band. |
| get_variants_by_efo_id | Get GWAS Catalog studies by EFO identifier |
| get_variants_by_efo_trait | Get GWAS Catalog variants by EFO traits |
| get_variants_by_gene_name | Get GWAS Catalog variants by gene name. |
| get_variants_by_genomic_range | Get GWAS Catalog variants by genomic range |
| get_variants_by_pubmed_id | Get GWAS Catalog variants by PubMed identifiers |
| get_variants_by_reported_trait | Get GWAS Catalog variants by reported traits |
| get_variants_by_study_id | Get GWAS Catalog variants by study identifiers |
| get_variants_by_variant_id | Get GWAS Catalog variants by variant identifiers |
| gwasrapidd-package | gwasrapidd: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS'... |
| is_association_id | Is a string a GWAS Catalog association accession ID? |
| is_ebi_reachable | Is the GWAS Catalog REST API server reachable? |
| is_efo_id | Is a string an EFO trait ID? |
| is_efo_id2 | Is a string an EFO trait ID in the broad sense? |
| is_embedded | Is the GWAS response wrapped in an '_embedded' object? |
| is_empty_str | Is string empty or an all whitespace string? |
| is_human_chromosome | Is a string a human chromosome name? |
| is_paginated | Is the GWAS response paginated? |
| is_pubmed_id | Is a string a PubMed ID? |
| is_rs_id | Is a string a valid rsID? |
| is_study_id | Is a string a GWAS Catalog study accession ID? |
| list_to_s4 | Convert a named list to an S4 object |
| loci_tbl | Creates a loci table. |
| lstjoin | Joins for lists. |
| metadata_lst | Generate a list to hold GWAS metadata |
| missing_to_na | Recursively map all missing values to 'NA'. |
| n | Number of GWAS Catalog entities |
| normalise_obj | Normalise a JSON-list. |
| object_type_from_url | Identify the GWAS object entity from the URL endpoint |
| open_in_dbsnp | Browse dbSNP from SNP identifiers. |
| open_in_gtex | Browse GTEx from SNP identifiers. |
| open_in_gwas_catalog | Browse GWAS Catalog entities from the GWAS Web Graphical User... |
| open_in_pubmed | Browse PubMed from PubMed identifiers. |
| peel_off_embedded | Peels off the _embedded tier from a JSON-list. |
| pipe | Pipe operator |
| platforms_tbl | Creates a platforms table. |
| publications_tbl | Creates a publications table. |
| recursive_apply | Simple rapply version that deals with NULL values. |
| reported_genes_tbl | Creates an authors' reported genes table. |
| risk_alleles_tbl | Creates a risk alleles table. |
| s4_to_list | Convert an S4 object into a list |
| setop | Set operations on GWAS Catalog objects. |
| set_testing_fast | Setup the environment to skip slow tests |
| set_testing_slow | Setup the environment to still run slow tests |
| skip_if_testing_is_fast | Skips a test if TEST_FAST is 'true' |
| studies | Constructor for the S4 studies object. |
| studies-class | An S4 class to represent a set of GWAS Catalog studies |
| studies_drop_na | Drop any NA studies. |
| studies_tbl | Creates a studies table. |
| study_to_association | Map a study id to an association id |
| study_to_trait | Map a study id to a EFO trait id |
| study_to_variant | Map a study id to a variant id |
| subset-associations | Subset an associations object |
| subset-studies | Subset a studies object |
| subset-traits | Subset a traits object |
| subset-variants | Subset a variants object |
| sure | Are you sure? |
| traits | Constructor for the S4 traits object. |
| traits-class | An S4 class to represent a set of GWAS Catalog EFO traits. |
| traits_drop_na | Drop any NA traits. |
| traits_tbl | Creates a traits tibble |
| trait_to_association | Map an EFO trait id to an association id |
| trait_to_study | Map an EFO trait id to a study id |
| trait_to_variant | Map an EFO trait id to a variant id |
| tws | Trim whitespace. |
| variant_name | Extract variant identifiers from strings of the form rs123-G |
| variants | Constructor for the S4 variants object. |
| variants-class | An S4 class to represent a set of GWAS Catalog variants |
| variants_drop_na | Drop any NA variants. |
| variants_tbl | Creates a variants table. |
| variant_to_association | Map a variant id to an association id |
| variant_to_study | Map a variant id to a study id |
| variant_to_trait | Map a variant id to an EFO trait |
| v_ensembl_ids_tbl | Creates a gene Ensembl identifiers table. |
| v_entrez_ids_tbl | Creates a gene Entrez identifiers table. |
| write_xlsx | Export a GWAS Catalog object to xlsx |
