Summix
Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data
Bioconductor version: Release (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")
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 | 2.12.0 |
| 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_2.12.0.tar.gz |
| Windows Binary (x86_64) | Summix_2.12.0.zip (64-bit only) |
| macOS Binary (x86_64) | Summix_2.12.0.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 |