Summix
This is the development version of Summix; for the stable release version, see Summix.
Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data
Bioconductor version: Development (3.20)
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("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 | ||
NEWS | Text | |
LICENSE | Text |
Details
biocViews | Genetics, Software, StatisticalMethod, WholeGenome |
Version | 2.11.0 |
In Bioconductor since | BioC 3.13 (R-4.1) (3.5 years) |
License | MIT + file LICENSE |
Depends | R (>= 4.3) |
Imports | dplyr, nloptr, magrittr, methods, tibble, tidyselect, BEDASSLE, scales, visNetwork, randomcoloR |
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_2.11.0.tar.gz |
Windows Binary (x86_64) | Summix_2.11.0.zip |
macOS Binary (x86_64) | Summix_2.11.0.tgz |
macOS Binary (arm64) | Summix_2.11.0.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 |