Man pages for ramiromagno/gwasrapidd
'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS' Catalog

add_object_tierAdds an element named <obj_type> to content sub-element.
allele_nameExtract allele names from strings of the form rs123-G
ancestral_groups_tblCreates an ancestral groups table.
ancestries_tblCreates an ancestries table.
associationsConstructor for the S4 associations object.
associations-classAn S4 class to represent a set of GWAS Catalog associations
associations_drop_naDrop any NA associations.
associations_tblCreates an associations table.
association_to_studyMap an association id to a study id
association_to_traitMap an association id to an EFO trait id
association_to_variantMap an association id to a variant id
bindBind GWAS Catalog objects
child_efo_idsGet all child terms of this trait in the EFO hierarchy
contains_question_markDoes a string contain a question mark?
countries_tblCreates a countries table.
cytogenetic_bandsGRCh38 human cytogenetic bands.
cytogenetic_band_to_genomic_rangeConvert a cytogenetic band string to genomic coordinates.
empty_to_naConverts an empty vector to a scalar NA
ensembl_ids_tblCreates an Ensembl gene identifiers' table.
entrez_ids_tblCreates an Entrez gene identifiers' table.
equal_lengthGrows vectors to match longest vector
exists_variantCheck if a variant exists in the Catalog.
extract_association_idExtract association identifiers from URLs
filter_by_idFilter GWAS Catalog objects by identifier.
filter_variants_by_standard_chromosomesFilter variants by standard human chromosomes.
gc_examplesgwasrapidd entities' examples
gc_getGet a GWAS Catalog resource
gc_requestRequest a GWAS Catalog REST API endpoint
gc_request_allRequest a paginated GWAS Catalog REST API endpoint
genomic_contexts_tblCreates a genomic contexts table.
genotyping_techs_tblCreates a genotyping technologies table.
get_associationsGet GWAS Catalog associations
get_associations_allGet all GWAS Catalog associations
get_associations_by_association_idGet GWAS Catalog associations by their association...
get_associations_by_efo_idGet GWAS Catalog associations by EFO identifier
get_associations_by_efo_traitGet GWAS Catalog associations by EFO traits
get_associations_by_pubmed_idGet GWAS Catalog associations by PubMed identifiers
get_associations_by_study_idGet GWAS Catalog associations by study identifiers
get_associations_by_variant_idGet GWAS Catalog associations by variant identifiers
get_child_efoGet all child terms of this trait in the EFO hierarchy
get_metadataGet GWAS Catalog metadata
get_studiesGet GWAS Catalog studies
get_studies_allGet all GWAS Catalog studies
get_studies_by_association_idGet GWAS Catalog studies by association identifiers
get_studies_by_efo_idGet GWAS Catalog studies by EFO identifier
get_studies_by_efo_traitGet GWAS Catalog studies by EFO traits
get_studies_by_efo_uriGet GWAS Catalog studies by EFO URIs
get_studies_by_full_pvalue_setGet GWAS Catalog studies by full summary statistics criterion
get_studies_by_pubmed_idGet GWAS Catalog studies by PubMed identifiers
get_studies_by_reported_traitGet GWAS Catalog studies by reported traits
get_studies_by_study_idGet GWAS Catalog studies by study identifiers
get_studies_by_user_requestedGet GWAS Catalog studies that have been requested by users or...
get_studies_by_variant_idGet GWAS Catalog studies by variant identifiers
get_traitsGet GWAS Catalog EFO traits
get_traits_allGet all GWAS Catalog EFO traits
get_traits_by_association_idGet GWAS Catalog traits by association identifiers
get_traits_by_efo_idGet GWAS Catalog traits by EFO identifier
get_traits_by_efo_traitGet GWAS Catalog traits by EFO traits
get_traits_by_efo_uriGet GWAS Catalog traits by EFO URIs
get_traits_by_pubmed_idGet GWAS Catalog traits by PubMed identifiers
get_traits_by_study_idGet GWAS Catalog traits by study identifiers
get_variantsGet GWAS Catalog variants
get_variants_allGet all GWAS Catalog variants
get_variants_by_association_idGet GWAS Catalog variants by their association identifiers
get_variants_by_cytogenetic_bandGet GWAS Catalog variants by cytogenetic band.
get_variants_by_efo_idGet GWAS Catalog studies by EFO identifier
get_variants_by_efo_traitGet GWAS Catalog variants by EFO traits
get_variants_by_gene_nameGet GWAS Catalog variants by gene name.
get_variants_by_genomic_rangeGet GWAS Catalog variants by genomic range
get_variants_by_pubmed_idGet GWAS Catalog variants by PubMed identifiers
get_variants_by_reported_traitGet GWAS Catalog variants by reported traits
get_variants_by_study_idGet GWAS Catalog variants by study identifiers
get_variants_by_variant_idGet GWAS Catalog variants by variant identifiers
gwasrapidd-packagegwasrapidd: 'REST' 'API' Client for the 'NHGRI'-'EBI' 'GWAS'...
is_association_idIs a string a GWAS Catalog association accession ID?
is_ebi_reachableIs the GWAS Catalog REST API server reachable?
is_efo_idIs a string an EFO trait ID?
is_efo_id2Is a string an EFO trait ID in the broad sense?
is_embeddedIs the GWAS response wrapped in an '_embedded' object?
is_empty_strIs string empty or an all whitespace string?
is_human_chromosomeIs a string a human chromosome name?
is_paginatedIs the GWAS response paginated?
is_pubmed_idIs a string a PubMed ID?
is_rs_idIs a string a valid rsID?
is_study_idIs a string a GWAS Catalog study accession ID?
list_to_s4Convert a named list to an S4 object
loci_tblCreates a loci table.
lstjoinJoins for lists.
metadata_lstGenerate a list to hold GWAS metadata
missing_to_naRecursively map all missing values to 'NA'.
nNumber of GWAS Catalog entities
normalise_objNormalise a JSON-list.
object_type_from_urlIdentify the GWAS object entity from the URL endpoint
open_in_dbsnpBrowse dbSNP from SNP identifiers.
open_in_gtexBrowse GTEx from SNP identifiers.
open_in_gwas_catalogBrowse GWAS Catalog entities from the GWAS Web Graphical User...
open_in_pubmedBrowse PubMed from PubMed identifiers.
peel_off_embeddedPeels off the _embedded tier from a JSON-list.
pipePipe operator
platforms_tblCreates a platforms table.
publications_tblCreates a publications table.
recursive_applySimple rapply version that deals with NULL values.
reported_genes_tblCreates an authors' reported genes table.
risk_alleles_tblCreates a risk alleles table.
s4_to_listConvert an S4 object into a list
setopSet operations on GWAS Catalog objects.
set_testing_fastSetup the environment to skip slow tests
set_testing_slowSetup the environment to still run slow tests
skip_if_testing_is_fastSkips a test if TEST_FAST is 'true'
studiesConstructor for the S4 studies object.
studies-classAn S4 class to represent a set of GWAS Catalog studies
studies_drop_naDrop any NA studies.
studies_tblCreates a studies table.
study_to_associationMap a study id to an association id
study_to_traitMap a study id to a EFO trait id
study_to_variantMap a study id to a variant id
subset-associationsSubset an associations object
subset-studiesSubset a studies object
subset-traitsSubset a traits object
subset-variantsSubset a variants object
sureAre you sure?
traitsConstructor for the S4 traits object.
traits-classAn S4 class to represent a set of GWAS Catalog EFO traits.
traits_drop_naDrop any NA traits.
traits_tblCreates a traits tibble
trait_to_associationMap an EFO trait id to an association id
trait_to_studyMap an EFO trait id to a study id
trait_to_variantMap an EFO trait id to a variant id
twsTrim whitespace.
variant_nameExtract variant identifiers from strings of the form rs123-G
variantsConstructor for the S4 variants object.
variants-classAn S4 class to represent a set of GWAS Catalog variants
variants_drop_naDrop any NA variants.
variants_tblCreates a variants table.
variant_to_associationMap a variant id to an association id
variant_to_studyMap a variant id to a study id
variant_to_traitMap a variant id to an EFO trait
v_ensembl_ids_tblCreates a gene Ensembl identifiers table.
v_entrez_ids_tblCreates a gene Entrez identifiers table.
write_xlsxExport a GWAS Catalog object to xlsx
ramiromagno/gwasrapidd documentation built on Jan. 3, 2024, 10:21 p.m.