Summix
This is the released version of Summix; for the devel version, see Summix.
Summix2: A suite of methods to estimate, adjust, and leverage substructure in genetic summary data
Bioconductor version: Release (3.23)
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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") 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 | 2.18.0 |
| In Bioconductor since | BioC 3.13 (R-4.1) (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_2.18.0.tar.gz |
| Windows Binary (x86_64) | Summix_2.18.0.zip (64-bit only) |
| macOS Binary (big-sur-x86_64) | Summix_2.18.0.tgz |
| macOS Binary (sonoma-arm64) | Summix_2.18.0.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 |