Summix
Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data
Bioconductor version: 3.23 · Package version: 2.18.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("Summix")Details
| Maintainer | Audrey Hendricks <audrey.hendricks@cuanschutz.edu> |
| Author | Audrey Hendricks [cre], Price Adelle [aut], Stoneman Haley [aut] |
| License | MIT + file LICENSE |
| Bug Reports | https://github.com/Bioconductor/Summix/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | Genetics, Software, StatisticalMethod, WholeGenome |
| Package Short Url | https://bioconductor.org/packages/Summix/ |
Citation
From within R, enter citation("Summix"):
Price Adelle, Stoneman Haley. Summix: Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data. doi:10.18129/B9.bioc.Summix, R package version 2.18.0, https://bioconductor.org/packages/Summix.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | Summix_2.18.0.tar.gz |
| Windows binary (x86_64) | Summix_2.18.0.zip |
| macOS binary (arm64) | Summix_2.18.0.tgz |
| macOS binary (x86_64) | Summix_2.18.0.tgz |
Dependencies
Depends: R (>= 4.3)
Imports: dplyr, nloptr, magrittr, methods, tibble, tidyselect, BEDASSLE, scales, visNetwork, randomcoloR
Suggests: rmarkdown, markdown, knitr, testthat (>= 3.0.0)