Summix
This package is for version 3.13 of Bioconductor; for the stable, up-to-date release version, see Summix.
Summix: A method to estimate and adjust for population structure in genetic summary data
Bioconductor version: 3.13
This package contains the Summix method for estimating and adjusting for ancestry in genetic summary allele frequency data. The function summix estimates reference ancestry proportions using a mixture model. The adjAF function produces ancestry adjusted allele frequencies for an observed sample with ancestry proportions matching a target person or sample.
Author: Audrey Hendricks [cre], Stoneman Haley [aut]
Maintainer: Audrey Hendricks <audrey.hendricks at ucdenver.edu>
citation("Summix")):
Installation
To install this package, start R (version "4.1") 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 | 1.0.3 |
| In Bioconductor since | BioC 3.13 (R-4.1) (3 years) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.1) |
| Imports | nloptr, methods |
| System Requirements | |
| URL | |
| Bug Reports | https://github.com/Bioconductor/Summix/issues |
See More
| Suggests | rmarkdown, markdown, knitr |
| 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_1.0.3.tar.gz |
| Windows Binary | Summix_1.0.3.zip (32- & 64-bit) |
| macOS 10.13 (High Sierra) | Summix_1.0.3.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 |
| Old Source Packages for BioC 3.13 | Source Archive |