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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>

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

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

Details

biocViews Genetics, Software, StatisticalMethod, WholeGenome
Version 2.9.1
In Bioconductor since BioC 3.13 (R-4.1) (3 years)
License MIT + file LICENSE
Depends R (>= 4.3)
Imports dplyr, nloptr, magrittr, methods, tibble, tidyselect
System Requirements
URL
Bug Reports https://github.com/Bioconductor/Summix/issues
See More
Suggests rmarkdown, markdown, knitr, testthat (>= 3.0.0)
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_2.9.1.tar.gz
Windows Binary Summix_2.9.1.zip
macOS Binary (x86_64) Summix_2.9.1.tgz
macOS Binary (arm64) Summix_2.9.1.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