NEWS

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lantern 0.99.0

• Initial Bioconductor submission.
• ancestry_split() splits a phased VCF into per-ancestry dosages using RFMix local ancestry, in "haplotype" (phased) or "dosage" (unphased) mode, for any number of populations. Dosage mode shrinks ambiguous mixed-ancestry splits toward each chromosome arm's global ancestry.
• write_ancestry_gds() / write_dosage_gds() write SeqArray GDS files.
• ancestry_smmat() runs ancestry-stratified GMMAT SMMAT gene tests and Cauchy-combines the per-ancestry p-values (cauchy_combine()).
• VCFs are read with bcftools when it is on PATH, otherwise with SeqArray. Choose one explicitly with options(lantern.vcf_reader = ...).
• Example dataset in inst/extdata (simulated; see inst/scripts/make_toy_data.R).