ASAFE

DOI: 10.18129/B9.bioc.ASAFE    

This package is for version 3.8 of Bioconductor; for the stable, up-to-date release version, see ASAFE.

Ancestry Specific Allele Frequency Estimation

Bioconductor version: 3.8

Given admixed individuals' bi-allelic SNP genotypes and ancestry pairs (where each ancestry can take one of three values) for multiple SNPs, perform an EM algorithm to deal with the fact that SNP genotypes are unphased with respect to ancestry pairs, in order to estimate ancestry-specific allele frequencies for all SNPs.

Author: Qian Zhang <qszhang at uw.edu>

Maintainer: Qian Zhang <qszhang at uw.edu>

Installation

To install this package, start R (version "3.5") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("ASAFE")

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("ASAFE")

 

PDF	R Script	ASAFE (Ancestry Specific Allele Frequency Estimation)
PDF		Reference Manual
Text		README
Text		NEWS

Details

biocViews	BiomedicalInformatics, ExperimentalDesign, Genetics, GenomeWideAssociation, LinkageDisequilibrium, SNP, Software
Version	1.8.0
In Bioconductor since	BioC 3.4 (R-3.3) (2.5 years)
License	Artistic-2.0
Depends	R (>= 3.2)
Imports
LinkingTo
Suggests	knitr, testthat
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

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

Source Package	ASAFE_1.8.0.tar.gz
Windows Binary	ASAFE_1.8.0.zip
Mac OS X 10.11 (El Capitan)	ASAFE_1.8.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/ASAFE
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/ASAFE
Package Short Url	http://bioconductor.org/packages/ASAFE/
Package Downloads Report	Download Stats