Summix

DOI: 10.18129/B9.bioc.Summix  

This is the development version of Summix; for the stable release version, see Summix.

Summix2: A method to estimate and adjust for substructure in genetic summary data

Bioconductor version: Development (3.19)

This package contains the Summix2 method for estimating and adjusting for substructure in genetic summary allele frequency data. The function summix() estimates reference group proportions using a mixture model. The adjAF() function produces adjusted allele frequencies for an observed group with reference group proportions matching a target individual or sample. The summix_local() function estimates local ancestry mixture proportions and performs selection scans in genetic summary data.

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

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

Installation

To install this package, start R (version "4.4") and enter:

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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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	2.9.1
In Bioconductor since	BioC 3.13 (R-4.1) (2.5 years)
License	MIT + file LICENSE
Depends	R (>= 4.3)
Imports	dplyr, nloptr, magrittr, methods, tibble, tidyselect
LinkingTo
Suggests	rmarkdown, markdown, knitr, testthat (>= 3.0.0)
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_2.9.1.tar.gz
Windows Binary	Summix_2.9.1.zip (64-bit only)
macOS Binary (x86_64)	Summix_2.9.1.tgz
macOS Binary (arm64)
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