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.

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

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Pipe operator