Package: CCAFE 1.4.0

Hayley Wolff

CCAFE: Case Control Allele Frequency Estimation

Functions to reconstruct case and control AFs from summary statistics. One function uses OR, NCase, NControl, and SE(log(OR)). The second function uses OR, NCase, NControl, and AF for the whole sample.

Authors:Hayley Wolff [cre, aut]

CCAFE_1.4.0.tar.gz
CCAFE_1.4.0.zip(r-4.7)CCAFE_1.4.0.zip(r-4.6)CCAFE_1.4.0.zip(r-4.5)
CCAFE_1.4.0.tgz(r-4.6-any)CCAFE_1.4.0.tgz(r-4.5-any)
CCAFE_1.4.0.tar.gz(r-4.7-any)CCAFE_1.4.0.tar.gz(r-4.6-any)
CCAFE_1.4.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
card.svg |card.png
CCAFE/json (API)
NEWS

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

Bug tracker:https://github.com/wolffha/ccafe/issues

Datasets:
  • sampleDat - PanUKBB and gnomAD Diabetes Data
  • vcf_sample - A VCF from this GWAS of Type 2 Diabetes https://doi.org/10.1038/s41588-018-0084-1. containing a subset of 10,000 variants

On BioConductor:CCAFE-1.5.0(bioc 3.24)CCAFE-1.4.0(bioc 3.23)

genomewideassociationcomparativegenomicsgeneticspreprocessingsnpsoftwarewholegenome

4.53 score 1 stars 17 scripts 248 downloads 3 exports 75 dependencies

Last updated from:91b20f3cc5 (on RELEASE_3_23). Checks:1 NOTE, 9 OK. Indexed: no.

TargetResultTimeFilesSyslog
bioc-checksNOTE166
linux-devel-x86_64OK234
source / vignettesOK295
linux-release-x86_64OK250
macos-release-arm64OK167
macos-oldrel-arm64OK130
windows-develOK151
windows-releaseOK176
windows-oldrelOK202
wasm-releaseOK163

Exports:CaseControl_AFCaseControl_SECCAFE_convertVCF

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsystibbletidyselectutf8VariantAnnotationvctrswithrXMLXVectoryaml

CCAFE Extra Details

Hayley Stoneman

Rendered fromCCAFE_Extra_Details.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-03-10
Started: 2024-10-02

CCAFE Vignette

Hayley Stoneman

Rendered fromCCAFE.Rmdusingknitr::rmarkdownon May 29 2026.

Last update: 2025-03-10
Started: 2024-10-02