Nothing
context("Merge maps")
test_that("merging maps correctly", {
##### Tetraploid
map1<-get_submap(solcap.dose.map[[1]], 1:5, reestimate.rf = FALSE, verbose = FALSE)
map2<-get_submap(solcap.dose.map[[1]], 6:15, reestimate.rf = FALSE, verbose = FALSE)
map3<-get_submap(solcap.dose.map[[1]], 16:30, reestimate.rf = FALSE, verbose = FALSE)
full.map<-get_submap(solcap.dose.map[[1]], 1:30, reestimate.rf = FALSE, verbose = FALSE)
s<-make_seq_mappoly(tetra.solcap, full.map$maps[[1]]$seq.num)
twopt <- est_pairwise_rf(input.seq = s)
merged.maps<-merge_maps(map.list = list(map1, map2, map3),
twopt = twopt,
thres.twopt = 3)
expect_equal(round(mean(unlist(merged.maps$maps[[1]]$seq.ph)),6), 2.495868)
best.phase <- merged.maps$maps[[1]]$seq.ph
names.id<-names(best.phase$P)
x1 <- compare_haplotypes(ploidy = 4, best.phase$P[names.id],
full.map$maps[[1]]$seq.ph$P[names.id])
x2 <- compare_haplotypes(ploidy = 4, best.phase$Q[names.id],
full.map$maps[[1]]$seq.ph$Q[names.id])
expect_true(x1$is.same.haplo)
expect_true(x2$is.same.haplo)
})
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