Nothing
context("rbind and cbind viterbi")
test_that("rbind.viterbi works for grav", {
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
map <- insert_pseudomarkers(grav2$gmap, step=1)
g <- viterbi(grav2, map, error_prob=0.002)
gA <- g[1:5,]
gB <- g[6:12,]
gC <- g[13:20,]
gAB <- g[1:12,]
gABC <- g[1:20,]
gBACA <- g[c(6:12, 1:5, 13:20, 1:5),]
expect_equal(rbind(gA, gB), gAB)
expect_equal(rbind(gA, gB, gC), gABC)
expect_equal(rbind(gB, gA, gC, gA), gBACA)
})
test_that("rbind.viterbi works for iron", {
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
map <- insert_pseudomarkers(iron$gmap, step=1)
g <- viterbi(iron, map, error_prob=0.002)
gA <- g[2:20,]
gB <- g[41:60,]
gC <- g[102:201,]
gAB <- g[c(2:20,41:60),]
gABC <- g[c(2:20,41:60,102:201),]
gBACA <- g[c(41:60,2:20,102:201,2:20),]
expect_equal(rbind(gA, gB), gAB)
expect_equal(rbind(gA, gB, gC), gABC)
expect_equal(rbind(gB, gA, gC, gA), gBACA)
})
test_that("cbind.viterbi works for grav", {
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
map <- insert_pseudomarkers(grav2$gmap, step=1)
g <- viterbi(grav2[1:10,], map, error_prob=0.002)
gA <- g[,1:2]
gB <- g[,5]
gC <- g[,3:4]
gAB <- g[,c(1:2,5)]
gABC <- g[,c(1,2,5,3,4)]
gBACA <- g[,c(5,1:2,3:4,1:2)]
expect_equal(cbind(gA, gB), gAB)
expect_equal(cbind(gA, gB, gC), gABC)
expect_equal(cbind(gB, gA, gC, gA), gBACA)
})
test_that("cbind.viterbi works for iron", {
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
map <- insert_pseudomarkers(iron$gmap, step=1)
g <- viterbi(iron[6:21,], map, error_prob=0.002)
gA <- g[,2:3]
gB <- g[,c(4,5,8)]
gC <- g[,c(19,"X")]
gAB <- g[,c(2:3,4,5,8)]
gABC <- g[,c(2:3,4,5,8,19,"X")]
gBACA <- g[,c(4,5,8,2,3,19,"X",2,3)]
expect_equal(cbind(gA, gB), gAB)
expect_equal(cbind(gA, gB, gC), gABC)
expect_equal(cbind(gB, gA, gC, gA), gBACA)
})
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