Nothing
context("subset_scan1")
test_that("subset_scan1 works for intercross with two phenotypes", {
# read data
iron <- read_cross2(system.file("extdata", "iron.zip", package="qtl2"))
# calculate genotype probabilities
map <- insert_pseudomarkers(iron$gmap, step=1)
probs <- calc_genoprob(iron, map, error_prob=0.002)
# grab phenotypes and covariates; ensure that covariates have names attribute
pheno <- iron$pheno
covar <- match(iron$covar$sex, c("f", "m")) # make numeric
names(covar) <- rownames(iron$covar)
Xcovar <- get_x_covar(iron)
# perform genome scan
out <- scan1(probs, pheno, addcovar=covar, Xcovar=Xcovar)
# subset one column
expected <- unclass(out)[,2,drop=FALSE]
attr(expected, "sample_size") <- attr(out, "sample_size")[2]
class(expected) <- c("scan1", "matrix")
expect_equal(subset(out, map, lodcolumn=2), expected)
# subset chr 2, 8, and 9
keep <- (map2chr(map) %in% c("2", "8", "9"))
expected <- unclass(out)[keep,,drop=FALSE]
attr(expected, "sample_size") <- attr(out, "sample_size")
class(expected) <- c("scan1", "matrix")
expect_equal(subset(out, map, chr=c("2", "8", "9")), expected)
# subset chr 2, 8, and 9 and lodcolumn 2
expected <- unclass(expected)[,2,drop=FALSE]
attr(expected, "sample_size") <- attr(out, "sample_size")[2]
class(expected) <- c("scan1", "matrix")
expect_equal(subset(out, map, c("2", "8", "9"), 2), expected)
})
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