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CCAFE (development version)

CCAFE

This is the development version of CCAFE; for the stable release version, see CCAFE.

Case Control Allele Frequency Estimation

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DOI: 10.18129/B9.bioc.CCAFE

Bioconductor version: Development (3.23)

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.

Author: Hayley Wolff [cre, aut]

Maintainer: Hayley Wolff <hayley.wolff at cuanschutz.edu>

Citation (from within R, enter citation("CCAFE")):

Installation

To install this package, start R (version "4.6") and enter:


if (!require("BiocManager", quietly = TRUE))
 install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
BiocManager::install("CCAFE")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("CCAFE")

CCAFE Extra Details HTML R Script

CCAFE Vignette HTML R Script

Reference Manual PDF

NEWS Text

Need some help? Ask on the Bioconductor Support site!

Details

biocViews ComparativeGenomics, Genetics, GenomeWideAssociation, Preprocessing, SNP, Software, WholeGenome

Version 1.3.0

In Bioconductor since BioC 3.21 (R-4.5) (0.5 years)

License GPL-3

Depends R (>= 4.4.0)

Imports dplyr, VariantAnnotation

System Requirements

URL https://github.com/wolffha/CCAFE/

Bug Reports https://github.com/wolffha/CCAFE/issues

See More

Suggests testthat (>= 3.0.0), rmarkdown, markdown, knitr, tidyverse, DescTools, cowplot, BiocStyle, GenomicRanges, SummarizedExperiment, S4Vectors, IRanges

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Package Archives

Follow Installation instructions to use this package in your R session.

Source Package CCAFE_1.3.0.tar.gz

Windows Binary (x86_64)

macOS Binary (x86_64)

macOS Binary (arm64)

Source Repository git clone https://git.bioconductor.org/packages/CCAFE

Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/CCAFE

Bioc Package Browser https://code.bioconductor.org/browse/CCAFE/

Package Short Url https://bioconductor.org/packages/CCAFE/

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