Summix

This package is for version 3.13 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: 3.13

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>

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

Installation

To install this package, start R (version "4.1") 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")
Summix.html HTML R Script
Reference Manual PDF
NEWS Text
LICENSE Text

Details

biocViews Genetics, Software, StatisticalMethod, WholeGenome
Version 1.0.3
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.1)
Imports nloptr, methods
System Requirements
URL
Bug Reports https://github.com/Bioconductor/Summix/issues
See More
Suggests rmarkdown, markdown, knitr
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 Summix_1.0.3.tar.gz
Windows Binary Summix_1.0.3.zip (32- & 64-bit)
macOS 10.13 (High Sierra) Summix_1.0.3.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
Old Source Packages for BioC 3.13 Source Archive