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-any)CCAFE_1.5.0.zip(r-4.6-any)CCAFE_1.5.0.zip(r-4.5-any)
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 356 downloads 3 exports 76 dependencies

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

TargetResultTimeFilesSyslog
bioc-checksNOTE174
linux-develOK353
source / vignettesOK473
linux-releaseOK286
macos-releaseOK174
macos-oldrelOK136
windows-develOK124
windows-releaseOK147
windows-oldrelOK141
wasm-releaseOK141

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