Package: CCAFE 1.5.0

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_1.5.0.tar.gz
CCAFE_1.5.0.zip(r-4.7)CCAFE_1.5.0.zip(r-4.6)CCAFE_1.5.0.zip(r-4.5)
CCAFE_1.5.0.tgz(r-4.6-any)CCAFE_1.5.0.tgz(r-4.5-any)
CCAFE_1.5.0.tar.gz(r-4.7-any)CCAFE_1.5.0.tar.gz(r-4.6-any)
CCAFE_1.5.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
CCAFE/json (API)

# Install 'CCAFE' in R:
install.packages('CCAFE', repos = c('https://bioc.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

4.56 score 1 stars 18 scripts 3 exports 76 dependencies

Last updated from:1905db01f8. Checks:1 NOTE, 9 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksNOTE184
linux-devel-x86_64OK245
source / vignettesOK291
linux-release-x86_64OK248
macos-release-arm64OK121
macos-oldrel-arm64OK156
windows-develOK152
windows-releaseOK164
windows-oldrelOK201
wasm-releaseOK167

Exports:CaseControl_AFCaseControl_SECCAFE_convertVCF

Dependencies:abindAnnotationDbiaskpassBHBiobaseBiocBaseUtilsBiocGenericsBiocIOBiocParallelBiostringsbitbit64bitopsblobBSgenomecachemcigarilloclicodetoolscpp11crayoncurlDBIDelayedArraydplyrfastmapformatRfutile.loggerfutile.optionsgenericsGenomicAlignmentsGenomicFeaturesGenomicRangesgluehttrIRangesjsonliteKEGGRESTlambda.rlatticelifecyclemagrittrMatrixMatrixGenericsmatrixStatsmemoisemimeopensslpillarpkgconfigpngR6RCurlrestfulrRhtslibrjsonrlangRsamtoolsRSQLitertracklayerS4ArraysS4VectorsSeqinfosnowSparseArraySummarizedExperimentsystibbletidyselectutf8VariantAnnotationvctrswithrXMLXVectoryaml

CCAFE Extra Details
Introduction | Simulated dataset | MAF vs AF | Minor alleles in CaseControl_SE | Examples in simulated data | Using total minor allele frequency in CaseControl_AF | Demonstration in simulations | Variants on sex chromosomes | Session Info
Rendered fromCCAFE_Extra_Details.Rmdusingknitr::rmarkdown

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

CCAFE Vignette
Introduction | Installation | Overview of CCAFE Functions | CaseControl_AF | CaseControl_AF() input | CaseControl_AF() output | CaseControl_SE | CaseControl_SE() input | CaseControl_SE() output | Examples | A quick demo of CaseControl_AF() | A quick demo of CaseControl_SE() | Integration with Bioconductor | Tabular data | VCF data | VCF Conversion Function | Session Information
Rendered fromCCAFE.Rmdusingknitr::rmarkdown

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