Summix

DOI: 10.18129/B9.bioc.Summix  

This package is for version 3.16 of Bioconductor; for the stable, up-to-date release version, see Summix.

Summix: A method to estimate and adjust for population structure in genetic summary data

Bioconductor version: 3.16

This package contains the Summix method for estimating and adjusting for ancestry in genetic summary allele frequency data. The function summix estimates reference ancestry proportions using a mixture model. The adjAF function produces ancestry adjusted allele frequencies for an observed sample with ancestry proportions matching a target person or sample.

Author: Audrey Hendricks [cre], Stoneman Haley [aut]

Maintainer: Audrey Hendricks <audrey.hendricks at ucdenver.edu>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("Summix")

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("Summix")

 

HTML	R Script	Summix.html
PDF		Reference Manual
Text		NEWS
Text		LICENSE

Details

biocViews	Genetics, Software, StatisticalMethod, WholeGenome
Version	2.4.0
In Bioconductor since	BioC 3.13 (R-4.1) (2 years)
License	MIT + file LICENSE
Depends	R (>= 4.1)
Imports	nloptr, methods
LinkingTo
Suggests	rmarkdown, markdown, knitr
SystemRequirements
Enhances
URL
BugReports	https://github.com/Bioconductor/Summix/issues
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	Summix_2.4.0.tar.gz
Windows Binary	Summix_2.4.0.zip
macOS Binary (x86_64)	Summix_2.4.0.tgz
macOS Binary (arm64)	Summix_2.4.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/Summix
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/Summix
Bioc Package Browser	https://code.bioconductor.org/browse/Summix/
Package Short Url	https://bioconductor.org/packages/Summix/
Package Downloads Report	Download Stats