Nothing
context("eff_neighbor")
#load data
colkas <- qtl::read.cross(format="csvs",dir="./",genfile="ColKas_geno.csv",phefile = "ColKas_pheno.csv",
na.strings = c("_"), estimate.map=TRUE, crosstype = "riself")
colkas <- colkas[1:2,1:50]
colkas_genoprob <- qtl::calc.genoprob(colkas, step=4)
x <- colkas$pheno[,2]
y <- colkas$pheno[,3]
smap_colkas <- data.frame(x,y)
s_colkas <- quantile(dist(smap_colkas),c(0.1*(0:10)))
test_that(
desc = "skip_AB_riself",
code = {
colkas_eff1 <- eff_neighbor(genoprobs=colkas_genoprob,
pheno=log(colkas$pheno[,5]+1),
smap=smap_colkas, scale=7,
addcovar=as.matrix(colkas$pheno[,7:9]), fig=FALSE)
expect_true(all(is.na(colkas_eff1$d1)))
expect_true(all(is.na(colkas_eff1$d2)))
}
)
#backcross
data("fake.bc",package="qtl")
fake_bc <- fake.bc[1:2,1:50]
smap_bc <- cbind(runif(qtl::nind(fake_bc),1,100),runif(qtl::nind(fake_bc),1,100))
genoprobs_bc <- qtl::calc.genoprob(fake_bc,step=4)
test_that(
desc = "symmetry_bc",
code = {
effect_bc <- eff_neighbor(genoprobs=genoprobs_bc,
pheno=fake_bc$pheno[,1],
smap=smap_bc, scale=59,
addcovar=as.matrix(cbind(fake_bc$pheno$sex,fake_bc$pheno$age)),
fig=FALSE)
expect_equal(effect_bc$a1, effect_bc$d1)
}
)
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