Nothing
context("calc_genoprob2")
suppressMessages(library(qtl))
test_that("backcross autosome", {
data(hyper)
chr <- c(1, 3, 4, 17, 19)
hyper <- hyper[chr,]
hyper <- convert2cross2(hyper)
pr <- calc_genoprob(hyper, error_prob=0.002, lowmem=TRUE)
pr2 <- calc_genoprob(hyper, error_prob=0.002, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("intercross autosome", {
data(listeria)
chr <- c(1, 4, 14, 18)
listeria <- listeria[chr,]
listeria <- convert2cross2(listeria)
map <- insert_pseudomarkers(listeria$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(listeria, map, error_prob=0.01, lowmem=TRUE)
pr2 <- calc_genoprob(listeria, map, error_prob=0.01, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("risib autosome", {
data(hyper)
chr <- c(1, 3, 4, 17, 19)
hyper <- hyper[chr,]
class(hyper)[1] <- "risib"
hyper <- convert2cross2(hyper)
map <- insert_pseudomarkers(hyper$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(hyper, map, error_prob=0.002, lowmem=TRUE)
pr2 <- calc_genoprob(hyper, map, error_prob=0.002, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("riself autosome", {
data(hyper)
chr <- c(1, 3, 4, 17, 19)
hyper <- hyper[chr,]
class(hyper)[1] <- "riself"
hyper <- convert2cross2(hyper)
map <- insert_pseudomarkers(hyper$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(hyper, map, error_prob=0.002, lowmem=TRUE)
pr2 <- calc_genoprob(hyper, map, error_prob=0.002, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("f2 X chr", {
data(fake.f2)
fake.f2 <- fake.f2["X",]
fake.f2 <- convert2cross2(fake.f2)
map <- insert_pseudomarkers(fake.f2$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(fake.f2, map, error_prob=0.01, lowmem=TRUE)
pr2 <- calc_genoprob(fake.f2, map, error_prob=0.01, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("bc X chr", {
data(hyper)
hyper <- hyper["X",]
# make it half female, half male
hyper$pheno$sex <- rep(c("female", "male"), nind(hyper)/2)
hyper <- convert2cross2(hyper)
map <- insert_pseudomarkers(hyper$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=TRUE)
pr2 <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("f2 X chr all males", {
data(fake.f2)
fake.f2 <- fake.f2["X",]
fake.f2$pheno$sex <- 1
fake.f2 <- convert2cross2(fake.f2)
map <- insert_pseudomarkers(fake.f2$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(fake.f2, map, error_prob=0.02, lowmem=TRUE)
pr2 <- calc_genoprob(fake.f2, map, error_prob=0.02, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("f2 X chr all females", {
data(fake.f2)
fake.f2 <- fake.f2["X",]
fake.f2$pheno$sex <- 0
fake.f2 <- convert2cross2(fake.f2)
map <- insert_pseudomarkers(fake.f2$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(fake.f2, map, error_prob=0.02, lowmem=TRUE)
pr2 <- calc_genoprob(fake.f2, map, error_prob=0.02, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("f2 X chr all females forw", {
data(fake.f2)
fake.f2 <- fake.f2["X",]
fake.f2$pheno$sex <- 0
fake.f2$pheno$pgm <- 0
fake.f2 <- convert2cross2(fake.f2)
map <- insert_pseudomarkers(fake.f2$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(fake.f2, map, error_prob=0.0001, lowmem=TRUE)
pr2 <- calc_genoprob(fake.f2, map, error_prob=0.0001, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("f2 X chr all females rev", {
data(fake.f2)
fake.f2 <- fake.f2["X",]
fake.f2$pheno$sex <- 0
fake.f2$pheno$pgm <- 1
fake.f2 <- convert2cross2(fake.f2)
map <- insert_pseudomarkers(fake.f2$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(fake.f2, map, error_prob=0.0001, lowmem=TRUE)
pr2 <- calc_genoprob(fake.f2, map, error_prob=0.0001, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("bc X chr all males", {
data(hyper)
hyper <- hyper["X",]
hyper <- convert2cross2(hyper)
map <- insert_pseudomarkers(hyper$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=TRUE)
pr2 <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("bc X chr all females", {
data(hyper)
hyper <- hyper["X",]
hyper$pheno$sex <- "female"
hyper <- convert2cross2(hyper)
map <- insert_pseudomarkers(hyper$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=TRUE)
pr2 <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("doubled haploids", {
data(hyper)
hyper <- hyper[1,]
hyper$pheno <- hyper$pheno[,1,drop=FALSE]
class(hyper)[1] <- "dh"
hyper <- convert2cross2(hyper)
map <- insert_pseudomarkers(hyper$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=TRUE)
pr2 <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("haploids calc_genoprob", {
data(hyper)
hyper <- hyper[2,]
hyper$pheno <- hyper$pheno[,1,drop=FALSE]
class(hyper)[1] <- "haploid"
hyper <- convert2cross2(hyper)
map <- insert_pseudomarkers(hyper$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=TRUE)
pr2 <- calc_genoprob(hyper, map, error_prob=0.02, lowmem=FALSE)
expect_equal(pr, pr2)
})
test_that("backcross autosome with markers at same location", {
grav2 <- read_cross2(system.file("extdata", "grav2.zip", package="qtl2"))
grav2 <- grav2[1:4,1]
# put some markers at same location
grav2$gmap[[1]][4] <- grav2$gmap[[1]][3]
pr <- calc_genoprob(grav2, err=0, lowmem=TRUE)
pr2 <- calc_genoprob(grav2, err=0, lowmem=FALSE)
expect_true( all(!is.na(pr[[1]])) )
expect_equal(pr, pr2)
})
test_that("calc_genoprob works when multi-core", {
skip_if(isnt_karl(), "this test only run locally")
data(hyper)
hyper2 <- convert2cross2(hyper)
pr <- calc_genoprob(hyper2, error_prob=0.002, lowmem=TRUE)
pr_mc <- calc_genoprob(hyper2, error_prob=0.002, cores=2, lowmem=TRUE)
expect_equal(pr_mc, pr)
pr2 <- calc_genoprob(hyper2, error_prob=0.002, lowmem=FALSE)
expect_equal(pr2, pr)
pr2_mc <- calc_genoprob(hyper2, error_prob=0.002, cores=2, lowmem=FALSE)
expect_equal(pr2_mc, pr)
data(listeria)
listeria2 <- convert2cross2(listeria)
map <- insert_pseudomarkers(listeria2$gmap, step=1, stepwidth="max")
pr <- calc_genoprob(listeria2, map, error_prob=0.01, lowmem=TRUE)
pr_mc <- calc_genoprob(listeria2, map, error_prob=0.01, cores=2, lowmem=TRUE)
expect_equal(pr_mc, pr)
pr2 <- calc_genoprob(listeria2, map, error_prob=0.01, lowmem=FALSE)
expect_equal(pr2, pr)
pr2_mc <- calc_genoprob(listeria2, map, error_prob=0.01, cores=2, lowmem=FALSE)
expect_equal(pr2_mc, pr)
})
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