Ancestry-Specific Rare Variant Association Analysis

Documentation for package ‘lantern’ version 0.99.1

ancestry_smmat	Run ancestry-stratified SMMAT + Cauchy combination (Step 3)
ancestry_split	Split a phased VCF by local ancestry (Step 1)
ancestry_split_dosage	Run ancestry splitting pipeline
ancestry_split_phased	Run phased ancestry splitting pipeline
cauchy_combine	Cauchy combination test for multiple p-values
read_bed_file	Read a PLINK .bed file of BED-encoded local ancestry calls
split_diploid	Split genotype matrix by ancestry
split_diploid_multi	Split unphased genotype matrix by ancestry for K populations
split_haplotype	Split phased haplotypes by ancestry
split_haplotype_multi	Split phased haplotypes into K population-specific dosage matrices
write_ancestry_gds	Write all populations of an ancestry split to GDS files (Step 2)
write_dosage_gds	Write an ancestry-specific dosage matrix to a SeqArray GDS file