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Summix

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


Bioconductor version: Release (3.18)

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 "4.3") 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 2.8.0
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
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Suggests rmarkdown, markdown, knitr
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Package Archives

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

Source Package Summix_2.8.0.tar.gz
Windows Binary Summix_2.8.0.zip
macOS Binary (x86_64) Summix_2.8.0.tgz
macOS Binary (arm64) Summix_2.8.0.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