ASAFE
This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see ASAFE.
Ancestry Specific Allele Frequency Estimation
Bioconductor version: 3.9
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("ASAFE")):
Installation
To install this package, start R (version "3.6") 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) | R Script | |
| Reference Manual | ||
| README | Text | |
| NEWS | Text |
Details
| biocViews | BiomedicalInformatics, ExperimentalDesign, Genetics, GenomeWideAssociation, LinkageDisequilibrium, SNP, Software |
| Version | 1.10.0 |
| In Bioconductor since | BioC 3.4 (R-3.3) (7.5 years) |
| License | Artistic-2.0 |
| Depends | R (>= 3.2) |
| Imports | |
| System Requirements | |
| URL |
See More
| Suggests | knitr, testthat |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | ASAFE_1.10.0.tar.gz |
| Windows Binary | ASAFE_1.10.0.zip |
| Mac OS X 10.11 (El Capitan) | ASAFE_1.10.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ASAFE |
| Source Repository (Developer Access) | git clone [email protected]:packages/ASAFE |
| Bioc Package Browser | https://code.bioconductor.org/browse/ASAFE/ |
| Package Short Url | https://bioconductor.org/packages/ASAFE/ |
| Package Downloads Report | Download Stats |
| Old Source Packages for BioC 3.9 | Source Archive |