CCAFE

This is the development version of CCAFE; to use it, please install the devel version of Bioconductor.

Case Control Allele Frequency Estimation

Bioconductor version: Development (3.21)

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 "4.5") 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	0.99.7
In Bioconductor since	BioC 3.21 (R-4.5)
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

Suggests	testthat (>= 3.0.0), rmarkdown, markdown, knitr, tidyverse, DescTools, cowplot, BiocStyle, GenomicRanges, SummarizedExperiment, S4Vectors, IRanges
Linking To
Enhances
Depends On Me
Imports Me
Suggests Me
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Build Report	Build Report

Package Archives

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

Source Package	CCAFE_0.99.7.tar.gz
Windows Binary (x86_64)	CCAFE_0.99.7.zip
macOS Binary (x86_64)	CCAFE_0.99.7.tgz
macOS Binary (arm64)	CCAFE_0.99.7.tgz
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/
Package Downloads Report	Download Stats