Nothing
context("convert2cross2")
suppressMessages(library(qtl))
test_that("convert2cross2 works appropriately for hyper data", {
data(hyper)
hyper2 <- convert2cross2(hyper)
ids <- as.character(1:nind(hyper))
# class and crosstype
expect_equal(class(hyper2), "cross2")
expect_equal(hyper2$crosstype, "bc")
# X chr
is_x <- rep(FALSE, nchr(hyper))
names(is_x) <- c(1:19, "X")
is_x["X"] <- TRUE
expect_equal(hyper2$is_x_chr, is_x)
# genotypes
for(i in seq(along=hyper$geno)) {
go <- hyper$geno[[i]]$data
if(is_x[i])
go <- reviseXdata("bc", "simple", getsex(hyper),
geno=go, cross.attr=attributes(hyper),
force=TRUE)
gn <- hyper2$geno[[i]]
expect_true(all(is.na(go) | go > 0))
go[is.na(go)] <- 0
rownames(go) <- ids
expect_equal(gn, go)
}
# gmap
gmap <- lapply(pull.map(hyper),
function(a) { class(a) <- "numeric"; a })
expect_equal(hyper2$gmap, gmap)
# sex
is_female <- rep(FALSE, nind(hyper))
names(is_female) <- ids
expect_equal(hyper2$is_female, is_female)
# cross_info
cross_info <- matrix(0L, ncol=1, nrow=nind(hyper))
rownames(cross_info) <- ids
expect_equal(hyper2$cross_info, cross_info)
# pheno
phe <- hyper$pheno[,1,drop=FALSE]
rownames(phe) <- ids
phe <- as.matrix(phe)
expect_equal(hyper2$pheno, phe)
# covar
covar <- hyper$pheno[,2,drop=FALSE]
rownames(covar) <- ids
expect_equal(hyper2$covar, covar)
})
test_that("convert2cross2 works appropriately for fake.f2 data", {
data(fake.f2)
fake.f2.2 <- convert2cross2(fake.f2)
ids <- as.character(1:nind(fake.f2))
# class and crosstype
expect_equal(class(fake.f2.2), "cross2")
expect_equal(fake.f2.2$crosstype, "f2")
# X chr
is_x <- rep(FALSE, nchr(fake.f2))
names(is_x) <- c(1:19, "X")
is_x["X"] <- TRUE
expect_equal(fake.f2.2$is_x_chr, is_x)
# genotypes
for(i in seq(along=fake.f2.2$geno)) {
go <- fake.f2$geno[[i]]$data
if(is_x[i])
go <- reviseXdata("f2", "simple", getsex(fake.f2),
geno=go, cross.attr=attributes(fake.f2))
gn <- fake.f2.2$geno[[i]]
expect_true(all(is.na(go) | go > 0))
go[is.na(go)] <- 0
rownames(go) <- ids
expect_equal(gn, go)
}
# gmap
gmap <- lapply(pull.map(fake.f2), function(a) { class(a) <- "numeric"; a })
expect_equal(fake.f2.2$gmap, gmap)
# sex
sexpgm <- getsex(fake.f2)
is_female <- (sexpgm$sex == 0)
names(is_female) <- ids
expect_equal(fake.f2.2$is_female, is_female)
# cross_info
cross_info <- as.matrix(sexpgm$pgm)
rownames(cross_info) <- ids
expect_equal(fake.f2.2$cross_info, cross_info)
# pheno
phe <- fake.f2$pheno[,1,drop=FALSE]
rownames(phe) <- ids
phe <- as.matrix(phe)
expect_equal(fake.f2.2$pheno, phe)
# covar
covar <- fake.f2$pheno[,2:3,drop=FALSE]
rownames(covar) <- ids
expect_equal(fake.f2.2$covar, covar)
})
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