# NOT RUN {
data(bowhead.snps)
data(bowhead.snp.position)
snps <- df2gtypes(bowhead.snps, ploidy = 2, description = "Bowhead SNPS")
summary(snps)
# Run PHASE on all data
phase.results <- phase(snps, bowhead.snp.position, num.iter = 100,
save.posterior = FALSE)
# Filter phase results
filtered.results <- phaseFilter(phase.results, thresh = 0.5)
# Convert phased genotypes to gtypes
ids <- rownames(filtered.results)
strata <- bowhead.snps$Stock[match(ids, bowhead.snps$LABID)]
filtered.df <- cbind(id = ids, strata = strata, filtered.results)
phased.snps <- df2gtypes(filtered.df, ploidy = 2, description = "Bowhead phased SNPs")
summary(phased.snps)
# }
# NOT RUN {
# }
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