Introduction | Installation | Example data | Step 1: split dosages by local ancestry | Step 2: write per-ancestry GDS files | Step 3: ancestry-stratified gene tests | Further reading | Session information
Package: lantern 0.99.0
Yu Wang
lantern: Ancestry-Specific Rare Variant Association Analysis
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 with shrinkage toward global ancestry, 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>.
Authors:
lantern_0.99.0.tar.gz
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lantern_0.99.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
lantern/json (API)
| # Install 'lantern' in R: |
| install.packages('lantern', repos = c('https://biocstaging.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/yuw444/lantern/issues
Pkgdown/docs site:https://yuw444.github.io
softwaregeneticsgenomewideassociationsnpvariantannotation
Last updated from:fd0703b3db. Checks:1 NOTE, 15 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| bioc-checks | NOTE | 174 | ||
| linux-devel-arm64 | OK | 133 | ||
| linux-devel-x86_64 | OK | 178 | ||
| source / vignettes | OK | 245 | ||
| linux-release-arm64 | OK | 175 | ||
| linux-release-x86_64 | OK | 167 | ||
| macos-release-arm64 | OK | 140 | ||
| macos-release-x86_64 | OK | 288 | ||
| macos-oldrel-arm64 | OK | 150 | ||
| macos-oldrel-x86_64 | OK | 199 | ||
| windows-devel-arm64 | OK | 234 | ||
| windows-devel-x86_64 | OK | 169 | ||
| windows-release-arm64 | OK | 231 | ||
| windows-release-x86_64 | OK | 138 | ||
| windows-oldrel-x86_64 | OK | 124 | ||
| wasm-release | OK | 117 |
Exports:ancestry_smmatancestry_splitancestry_split_dosageancestry_split_phasedcauchy_combineread_bed_filesplit_diploidsplit_diploid_multisplit_haplotypesplit_haplotype_multiwrite_ancestry_gdswrite_dosage_gds
Dependencies:BiocGenericsBiostringscrayondata.tabledigestgdsfmtgenericsGenomicRangesIRangesS4VectorsSeqArraySeqinfoXVector
Getting started with lantern
Last update: 2026-10-06
Started: 2026-10-06
Split intuition: matrix examples for two and more populations
Overview | Part A: Two populations | A.1 Unphased (dosage) split — split_diploid() | A.2 Phased (haplotype) split — split_haplotype() | Part B: More than two populations | B.1 Unphased (dosage) split — split_diploid_multi() | B.2 Phased (haplotype) split — split_haplotype_multi() | B.3 Four- and five-population extension | Part C: GLA shrinkage — when ambiguous carriers dominate | Session information
Last update: 2026-10-06
Started: 2026-07-17
Toy example: splitting a VCF + MSP file (two and more populations)
Overview | Part A: Two populations | Part B: More than two populations (K = 4) | Session information
Last update: 2026-10-06
Started: 2026-07-17
Real data: chr19 association testing with binary, continuous, and count phenotypes
Overview | 1 Gene-group file and kinship | 2 Binary phenotype (family = binomial()) | 3 Continuous phenotype (family = gaussian()) | 4 Count phenotype (family = poisson()) | 5 Adjusting for covariates | 6 Where to get gene-group files for other species/builds | 7 Other ways to adapt this to your own data
Last update: 2026-07-19
Started: 2026-07-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Run ancestry-stratified SMMAT + Cauchy combination (Step 3) | ancestry_smmat |
| Split a phased VCF by local ancestry (Step 1) | ancestry_split |
| Run ancestry splitting pipeline | ancestry_split_dosage |
| Run phased ancestry splitting pipeline | ancestry_split_phased |
| Cauchy combination test for multiple p-values | cauchy_combine |
| Read a PLINK .bed file of BED-encoded local ancestry calls | read_bed_file |
| Split genotype matrix by ancestry | split_diploid |
| Split unphased genotype matrix by ancestry for K populations | split_diploid_multi |
| Split phased haplotypes by ancestry | split_haplotype |
| Split phased haplotypes into K population-specific dosage matrices | split_haplotype_multi |
| Write all populations of an ancestry split to GDS files (Step 2) | write_ancestry_gds |
| Write an ancestry-specific dosage matrix to a SeqArray GDS file | write_dosage_gds |