lantern
This is the development version of lantern; to use it, please install the devel version of Bioconductor.
Ancestry-Specific Rare Variant Association Analysis
Bioconductor version: Development (3.24)
Ancestry-specific rare variant burden testing for admixed populations. Splits genotype dosages by local ancestry (as inferred by 'RFMix') into per-ancestry dosages, using either phased haplotypes or unphased genotypes, where ambiguous mixed-ancestry heterozygotes are split with shrinkage toward 1/2, and writes them to 'SeqArray' GDS files. Ancestry-stratified gene-level tests are then run with the 'SMMAT' framework of Chen et al. (2019) <doi:10.1016/j.ajhg.2018.12.012> as implemented in 'GMMAT', and the per-ancestry p-values are combined with the Cauchy combination test of Liu and Xie (2020) <doi:10.1080/01621459.2018.1554485>.
Author: Yu Wang [aut, cre], Bjoernar Tuftin [aut], Paul Auer [aut]
Maintainer: Yu Wang <ywang at mcw.edu>
citation("lantern")):Yu Wang, Bjoernar Tuftin, Paul Auer. lantern: Ancestry-Specific Rare Variant Association Analysis. doi:10.18129/B9.bioc.lantern, R package version 0.99.1, https://bioconductor.org/packages/lantern.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("lantern")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("lantern")| Getting started with lantern | HTML |
| Real data: chr19 association testing with binary, continuous, and count phenotypes | HTML |
| Split intuition: matrix examples for two and more populations | HTML |
| Toy example: splitting a VCF + MSP file (two and more populations) | HTML |
| Reference Manual | |
| NEWS | Text |
Details
| biocViews | Genetics, GenomeWideAssociation, SNP, Software, VariantAnnotation |
| Version | 0.99.1 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | data.table, GMMAT, SeqArray, SeqVarTools, stats, utils |
| System Requirements | bcftools (>= 1.10) (optional; faster VCF reading and BCF input) |
| URL | https://yuw444.github.io/lantern/ https://github.com/yuw444/lantern |
| Bug Reports | https://github.com/yuw444/lantern/issues |
See More
| Suggests | BiocStyle, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/lantern |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/lantern |
| Package Short Url | https://bioconductor.org/packages/lantern/ |
| Package Downloads Report | Download Stats |