Package: quincunx 0.1.10

Ramiro Magno

quincunx: REST API Client for the 'PGS' Catalog

Programmatic access to the 'PGS' Catalog. This package provides easy access to 'PGS' Catalog data by accessing the REST API <https://www.pgscatalog.org/rest/>.

Authors:Ramiro Magno [aut, cre], Isabel Duarte [aut], Ana-Teresa Maia [aut], CINTESIS [cph, fnd], Pattern Institute [cph, fnd]

quincunx_0.1.10.tar.gz
quincunx_0.1.10.zip(r-4.7)quincunx_0.1.10.zip(r-4.6)quincunx_0.1.10.zip(r-4.5)
quincunx_0.1.10.tgz(r-4.6-any)quincunx_0.1.10.tgz(r-4.5-any)
quincunx_0.1.10.tar.gz(r-4.7-any)quincunx_0.1.10.tar.gz(r-4.6-any)
quincunx_0.1.10.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
quincunx/json (API)
NEWS

# Install 'quincunx' in R:
install.packages('quincunx', repos = c('https://patterninstitute.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/ramiromagno/quincunx/issues

Pkgdown/docs site:https://rmagno.eu

Datasets:

On CRAN:

Conda:

gwaspolygenic-risk-scorespolygenic-scores

2.98 score 8 stars 24 scripts 102 downloads 35 exports 48 dependencies

Last updated from:cda2544c27. Checks:9 OK. Indexed: no.

TargetResultTimeFilesSyslog
linux-devel-x86_64OK153
source / vignettesOK190
linux-release-x86_64OK148
macos-release-arm64OK107
macos-oldrel-arm64OK89
windows-develOK108
windows-releaseOK105
windows-oldrelOK87
wasm-releaseOK119

Exports:bindclear_cacheget_ancestry_categoriesget_cohortsget_performance_metricsget_publicationsget_releasesget_sample_setsget_scoresget_trait_categoriesget_traitsintersectnopen_in_dbsnpopen_in_pgs_catalogopen_in_pubmedpgp_to_pgspgp_to_ppmpgp_to_psspgs_to_pgppgs_to_ppmpgs_to_psspgs_to_studyppm_to_pgpppm_to_pgsppm_to_psspss_to_pgppss_to_pgspss_to_ppmread_scoring_filesetdiffsetequalstudy_to_pgsunionwrite_xlsx

Dependencies:askpassassertthatbitbit64cachemclicliprcpp11crayoncurldplyrfastmapgenericsgluehmshttrjsonlitelifecyclelubridatemagrittrmemoisemimeopensslpillarpkgconfigprettyunitsprogresspurrrR6readrrlangrvestselectrstringistringrsystibbletidyjsontidyrtidyselecttimechangetzdbutf8vctrsvroomwithrwritexlxml2

Readme and manuals

Help Manual

Help pageTopics
Ancestry categories and classesancestry_categories
Bind PGS Catalog objectsbind
Clear quincunx cache of memoised functionsclear_cache
An S4 class to represent a set of cohortscohorts-class
Get ancestry categories and classesget_ancestry_categories
Get PGS Catalog Cohortsget_cohorts
Get PGS Catalog Performance Metricsget_performance_metrics
Get PGS Catalog Publicationsget_publications
Get PGS Catalog Releasesget_releases
Get PGS Catalog Sample Setsget_sample_sets
Get PGS Catalog Scoresget_scores
Get PGS Catalog Trait Categoriesget_trait_categories
Get PGS Catalog Traitsget_traits
Number of PGS Catalog entitiesn n,cohorts-method n,performance_metrics-method n,publications-method n,releases-method n,sample_sets-method n,scores-method n,traits-method n,trait_categories-method
Browse dbSNP from SNP identifiers.open_in_dbsnp
Browse PGS Catalog entities from the PGS Catalog Web Graphical User Interfaceopen_in_pgs_catalog
Browse PubMed from PubMed identifiers.open_in_pubmed
An S4 class to represent a set of PGS Catalog Performance Metricsperformance_metrics-class
Map PGP identifiers to PGS identifierspgp_to_pgs
Map PGP identifiers to PPM identifierspgp_to_ppm
Map PGP identifiers to PSS identifierspgp_to_pss
Map PGS identifiers to PGP identifierspgs_to_pgp
Map PGS identifiers to PPM identifierspgs_to_ppm
Map PGS identifiers to PSS identifierspgs_to_pss
Map PGS identifiers to GWAS study identifierspgs_to_study
Map PPM identifiers to PGP identifiersppm_to_pgp
Map PPM identifiers to PGS identifiersppm_to_pgs
Map PPM identifiers to PSS identifiersppm_to_pss
Map PSS identifiers to PGP identifierspss_to_pgp
Map PSS identifiers to PGS identifierspss_to_pgs
Map PSS identifiers to PPM identifierspss_to_ppm
An S4 class to represent a set of PGS Catalog Publicationspublications-class
Read a polygenic scoring fileread_scoring_file
An S4 class to represent a set of PGS Catalog Releasesreleases-class
An S4 class to represent a set of PGS Catalog Sample Setssample_sets-class
An S4 class to represent a set of PGS Catalog Polygenic Scoresscores-class
Set operations on PGS Catalog objectsintersect setdiff setequal setop union
Study stagesstages
Map GWAS studies identifiers to PGS identifiersstudy_to_pgs
An S4 class to represent a set of PGS Catalog Trait Categoriestrait_categories-class
An S4 class to represent a set of PGS Catalog Traitstraits-class
Export a PGS Catalog object to xlsxwrite_xlsx