Man pages for maialab/quincunx
REST API Client for the 'PGS' Catalog
| ancestry_categories | Ancestry categories and classes |
| bind | Bind PGS Catalog objects |
| clear_cache | Clear quincunx cache of memoised functions |
| cohorts | Constructor for the S4 cohorts object. |
| cohorts-class | An S4 class to represent a set of cohorts |
| collect_pgs_ids | Collect development and evaluation pgs_ids |
| collect_samples | Collect samples_variants and samples_training |
| contains_question_mark | Does a string contain a question mark? |
| count | Extract the count field from a JSON response |
| filter_by_id | Filter PGS Catalog objects by identifier. |
| first_non_na | Returns the position of the first non-NA value |
| get_ancestry_categories | Get ancestry categories and classes |
| get_ancestry_symbol_mappings | Get PGS Catalog Ancestry Symbol Mappings |
| get_cohorts | Get PGS Catalog Cohorts |
| get_performance_metrics | Get PGS Catalog Performance Metrics |
| get_publications | Get PGS Catalog Publications |
| get_releases | Get PGS Catalog Releases |
| get_sample_sets | Get PGS Catalog Sample Sets |
| get_scores | Get PGS Catalog Scores |
| get_trait_categories | Get PGS Catalog Trait Categories |
| get_traits | Get PGS Catalog Traits |
| is_paginated | Is the response paginated? |
| is_pgs_id | Is a string a PGS Catalog identifier? |
| is_pubmed_id | Is a string a PubMed ID? |
| list_to_s4 | Convert a named list to an S4 object |
| msg_400 | Pretty printing of 404 error |
| msg_404 | Pretty printing of 404 error |
| msg_empty | Pretty printing of empty response |
| n | Number of PGS Catalog entities |
| no_msg | Pretty printing of no error message |
| n_pages | Number of pages |
| nr_to_na | Convert NR (Not Recorded) to NA (Not Available) |
| offsets | Generate offset values |
| open_in_dbsnp | Browse dbSNP from SNP identifiers. |
| open_in_pgs_catalog | Browse PGS Catalog entities from the PGS Catalog Web... |
| open_in_pubmed | Browse PubMed from PubMed identifiers. |
| performance_metrics | Constructor for the S4 performance_metrics object. |
| performance_metrics-class | An S4 class to represent a set of PGS Catalog Performance... |
| pgp_to_pgs | Map PGP identifiers to PGS identifiers |
| pgp_to_ppm | Map PGP identifiers to PPM identifiers |
| pgp_to_pss | Map PGP identifiers to PSS identifiers |
| pgs_server | PGS REST API server |
| pgs_to_pgp | Map PGS identifiers to PGP identifiers |
| pgs_to_ppm | Map PGS identifiers to PPM identifiers |
| pgs_to_pss | Map PGS identifiers to PSS identifiers |
| pgs_to_study | Map PGS identifiers to GWAS study identifiers |
| pipe | Pipe operator |
| ppm_to_pgp | Map PPM identifiers to PGP identifiers |
| ppm_to_pgs | Map PPM identifiers to PGS identifiers |
| ppm_to_pss | Map PPM identifiers to PSS identifiers |
| pss_to_pgp | Map PSS identifiers to PGP identifiers |
| pss_to_pgs | Map PSS identifiers to PGS identifiers |
| pss_to_ppm | Map PSS identifiers to PPM identifiers |
| publications | Constructor for the S4 publications object. |
| publications-class | An S4 class to represent a set of PGS Catalog Publications |
| read_scoring_file | Read a polygenic scoring file |
| releases | Constructor for the S4 releases object. |
| releases-class | An S4 class to represent a set of PGS Catalog Releases |
| remap_id | Remap identifiers |
| request | Request a resource from the PGS REST API |
| request_all | Request a paginated resource from the PGS REST API |
| request_warning | Pretty printing of http error |
| s4_to_list | Convert an S4 object into a list |
| sample_sets | Constructor for the S4 sample_sets object. |
| sample_sets-class | An S4 class to represent a set of PGS Catalog Sample Sets |
| scores | Constructor for the S4 scores object. |
| scores-class | An S4 class to represent a set of PGS Catalog Polygenic... |
| setop | Set operations on PGS Catalog objects |
| stages | Study stages |
| study_to_pgs | Map GWAS studies identifiers to PGS identifiers |
| subset-cohorts | Subset a cohorts object |
| subset-performance_metrics | Subset a performance_metrics object |
| subset-publications | Subset a publications object |
| subset-releases | Subset a releases object |
| subset-sample_sets | Subset a sample_sets object |
| subset-scores | Subset a scores object |
| subset-trait_categories | Subset a trait_categories object |
| subset-traits | Subset a traits object |
| sure | Are you sure? |
| trait_categories | Constructor for the S4 trait_categories object. |
| trait_categories-class | An S4 class to represent a set of PGS Catalog Trait... |
| traits | Constructor for the S4 traits object. |
| traits-class | An S4 class to represent a set of PGS Catalog Traits |
| user_agent_id | User agent identification |
| write_xlsx | Export a PGS Catalog object to xlsx |
