Function reference • gwasrapidd

GWAS Catalog Entities

S4 classes for studies, associations, variants and traits

studies-class: An S4 class to represent a set of GWAS Catalog studies

associations-class: An S4 class to represent a set of GWAS Catalog associations

variants-class: An S4 class to represent a set of GWAS Catalog variants

traits-class: An S4 class to represent a set of GWAS Catalog EFO traits.

Get GWAS Catalog Entities

Receive data from the GWAS Catalog REST API.

get_studies(): Get GWAS Catalog studies

get_associations(): Get GWAS Catalog associations

get_variants(): Get GWAS Catalog variants

get_traits(): Get GWAS Catalog EFO traits

get_metadata(): Get GWAS Catalog metadata

Subset GWAS Catalog Entities

Extract specific observations from studies, associations, variants or traits.

`[`(<studies>,<missing>,<missing>,<missing>) `[`(<studies>,<numeric>,<missing>,<missing>) `[`(<studies>,<character>,<missing>,<missing>): Subset a studies object

`[`(<associations>,<missing>,<missing>,<missing>) `[`(<associations>,<numeric>,<missing>,<missing>) `[`(<associations>,<character>,<missing>,<missing>): Subset an associations object

`[`(<variants>,<missing>,<missing>,<missing>) `[`(<variants>,<numeric>,<missing>,<missing>) `[`(<variants>,<character>,<missing>,<missing>): Subset a variants object

`[`(<traits>,<missing>,<missing>,<missing>) `[`(<traits>,<numeric>,<missing>,<missing>) `[`(<traits>,<character>,<missing>,<missing>): Subset a traits object

Data Wrangling of GWAS Catalog Entities

S4 methods for combining and tallying studies, associations, variants and traits.

n(): Number of GWAS Catalog entities

bind(): Bind GWAS Catalog objects

union() intersect() setdiff() setequal(): Set operations on GWAS Catalog objects.

Accession identifier mapping

Translate accession identifiers between studies, associations, variants and traits.

study_to_association(): Map a study id to an association id

study_to_variant(): Map a study id to a variant id

study_to_trait(): Map a study id to a EFO trait id

association_to_study(): Map an association id to a study id

association_to_variant(): Map an association id to a variant id

association_to_trait(): Map an association id to an EFO trait id

variant_to_study(): Map a variant id to a study id

variant_to_association(): Map a variant id to an association id

variant_to_trait(): Map a variant id to an EFO trait

trait_to_study(): Map an EFO trait id to a study id

trait_to_association(): Map an EFO trait id to an association id

trait_to_variant(): Map an EFO trait id to a variant id

Get data outside of GWAS Catalog

Functions to provide easy access to other web resources.

get_child_efo(): Get all child terms of this trait in the EFO hierarchy

Easily navigate web resources

Functions that allow you to quickly browse linked information.

open_in_pubmed(): Browse PubMed from PubMed identifiers.

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 Interface

Check functions

Test and diagnose common impediments.

is_ebi_reachable(): Is the GWAS Catalog REST API server reachable?

exists_variant(): Check if a variant exists in the Catalog.

Datasets

Datasets shipped with gwasrapidd

cytogenetic_bands: GRCh38 human cytogenetic bands.

studies_ex01 studies_ex02 associations_ex01 associations_ex02 variants_ex01 variants_ex02 traits_ex01 traits_ex02: gwasrapidd entities' examples

Miscellaneous

Other functions

%>%: Pipe operator

write_xlsx(): Export a GWAS Catalog object to xlsx