Nothing
context("scan1max")
test_that("scan1max works", {
iron <- read_cross2( system.file("extdata", "iron.zip", package="qtl2") )
iron <- iron[,c("1", "19", "X")]
Xc <- get_x_covar(iron)
X <- Xc[,1]
map <- insert_pseudomarkers(iron$gmap, step=2.5)
pr <- calc_genoprob(iron, map, error_prob=0.002)
k <- calc_kinship(pr)
k_loco <- calc_kinship(pr, "loco")
chr <- factor(rep(names(map), sapply(map, length)), names(map))
out <- scan1(pr, iron$pheno)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
attr(expected, "sample_size") <- attr(expected_bychr, "sample_size") <- attr(out, "sample_size")
expect_equal(scan1max(pr, iron$pheno), expected)
expect_equal(scan1max(pr, iron$pheno, by_chr=TRUE), expected_bychr)
out <- scan1(pr, iron$pheno, Xcovar=Xc)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
attr(expected, "sample_size") <- attr(expected_bychr, "sample_size") <- attr(out, "sample_size")
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc), expected)
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, by_chr=TRUE), expected_bychr)
out <- scan1(pr, iron$pheno, Xcovar=Xc, addcovar=X)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
attr(expected, "sample_size") <- attr(expected_bychr, "sample_size") <- attr(out, "sample_size")
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, addcovar=X), expected)
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, addcovar=X, by_chr=TRUE), expected_bychr)
out <- scan1(pr, iron$pheno, Xcovar=Xc, kinship=k)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
for(at in c("sample_size", "hsq")) {
attr(expected, at) <- attr(expected_bychr, at) <- attr(out, at)
}
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, kinship=k), expected)
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, kinship=k, by_chr=TRUE), expected_bychr)
out <- scan1(pr, iron$pheno, Xcovar=Xc, addcovar=X, kinship=k_loco)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
for(at in c("sample_size", "hsq")) {
attr(expected, at) <- attr(expected_bychr, at) <- attr(out, at)
}
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, addcovar=X, kinship=k_loco), expected)
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, addcovar=X, kinship=k_loco, by_chr=TRUE), expected_bychr)
})
test_that("scan1max works with multicore", {
skip_if(isnt_karl(), "this test only run locally")
iron <- read_cross2( system.file("extdata", "iron.zip", package="qtl2") )
iron <- iron[,c("1", "19", "X")]
Xc <- get_x_covar(iron)
X <- Xc[,1]
map <- insert_pseudomarkers(iron$gmap, step=2.5)
pr <- calc_genoprob(iron, map, error_prob=0.002)
k <- calc_kinship(pr)
k_loco <- calc_kinship(pr, "loco")
chr <- factor(rep(names(map), sapply(map, length)), names(map))
out <- scan1(pr, iron$pheno, cores=2)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
attr(expected, "sample_size") <- attr(expected_bychr, "sample_size") <- attr(out, "sample_size")
expect_equal(scan1max(pr, iron$pheno, cores=2), expected)
expect_equal(scan1max(pr, iron$pheno, by_chr=TRUE, cores=2), expected_bychr)
out <- scan1(pr, iron$pheno, Xcovar=Xc, cores=2)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
attr(expected, "sample_size") <- attr(expected_bychr, "sample_size") <- attr(out, "sample_size")
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, cores=2), expected)
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, by_chr=TRUE, cores=2), expected_bychr)
out <- scan1(pr, iron$pheno, Xcovar=Xc, addcovar=X, cores=2)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
attr(expected, "sample_size") <- attr(expected_bychr, "sample_size") <- attr(out, "sample_size")
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, addcovar=X, cores=2), expected)
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, addcovar=X, by_chr=TRUE, cores=2), expected_bychr)
out <- scan1(pr, iron$pheno, Xcovar=Xc, kinship=k, cores=2)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
for(at in c("sample_size", "hsq")) {
attr(expected, at) <- attr(expected_bychr, at) <- attr(out, at)
}
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, kinship=k, cores=2), expected)
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, kinship=k, by_chr=TRUE, cores=2), expected_bychr)
out <- scan1(pr, iron$pheno, Xcovar=Xc, addcovar=X, kinship=k_loco, cores=2)
expected <- apply(out, 2, max, na.rm=TRUE)
expected_bychr <- apply(out, 2, tapply, chr, max, na.rm=TRUE)
for(at in c("sample_size", "hsq")) {
attr(expected, at) <- attr(expected_bychr, at) <- attr(out, at)
}
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, addcovar=X, kinship=k_loco, cores=2), expected)
expect_equal(scan1max(pr, iron$pheno, Xcovar=Xc, addcovar=X, kinship=k_loco, by_chr=TRUE, cores=2),
expected_bychr)
})
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