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ASAFE

Ancestry Specific Allele Frequency Estimation


Bioconductor version: Release (3.18)

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>

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

Installation

To install this package, start R (version "4.3") and enter:


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

Details

biocViews BiomedicalInformatics, ExperimentalDesign, Genetics, GenomeWideAssociation, LinkageDisequilibrium, SNP, Software
Version 1.28.0
In Bioconductor since BioC 3.4 (R-3.3) (7.5 years)
License Artistic-2.0
Depends R (>= 3.2)
Imports
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Suggests knitr, testthat
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Package Archives

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

Source Package ASAFE_1.28.0.tar.gz
Windows Binary ASAFE_1.28.0.zip
macOS Binary (x86_64) ASAFE_1.28.0.tgz
macOS Binary (arm64) ASAFE_1.28.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/ASAFE
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/ASAFE
Bioc Package Browser https://code.bioconductor.org/browse/ASAFE/
Package Short Url https://bioconductor.org/packages/ASAFE/
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