Nothing
context("maxmarg")
test_that("maxmarg works for F2 data", {
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
iron <- iron[,8] # only chr 8
map <- insert_pseudomarkers(iron$gmap, step=2.5)
pr <- calc_genoprob(iron, map, error_prob=0.01)
z <- maxmarg(pr, minprob=0)
g <- z[[1]]
expected <- apply(pr[[1]], c(1,3), function(a) seq(along=a)[a==max(a)])
expect_equal(g, expected)
# single locus
zz <- maxmarg(pr, map, minprob=0, chr="8", pos=45.5)
expect_equal(zz, g[,"D8Mit40"])
# repeat with minprob=0.95
z <- maxmarg(pr, minprob=0.95)
g <- z[[1]]
expected <- apply(pr[[1]], c(1,3), function(a) { b <- max(a); ifelse(b > 0.95, which.max(a), NA) })
expect_equal(g, expected)
# single locus
zz <- maxmarg(pr, map, minprob=0.95, chr="8", pos=45.5)
expect_equal(zz, g[,"D8Mit40"])
# repeat with return_value="genotypes"
zchar <- maxmarg(pr, minprob=0.95, return_char=TRUE)
gchar <- g;gchar[,1:ncol(g)] <- c("SS", "SB", "BB")[g]
expect_equal(zchar[[1]], gchar)
# single locus
zzchar <- maxmarg(pr, map, minprob=0.95, chr="8", pos=45.5, return_char=TRUE)
gg <- c("SS", "SB", "BB")[zz]
names(gg) <- names(zz)
expect_equal(zzchar, gg)
})
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