Nothing
context("genoprobs columns to drop")
test_that("genoprobs_cols2drop works", {
# load example data from R/qtl
library(qtl)
data(fake.f2)
fake.f2 <- fake.f2[c(18,19,"X"),] # subset chromosomes
fake.f2 <- convert2cross2(fake.f2)
# calculate genoprobs
pr <- calc_genoprob(fake.f2)
# just X chromosome
expect_equal(genoprobs_col2drop(pr$X), numeric(0))
# all chromosomes
expected <- vector("list", length(pr))
names(expected) <- names(pr)
for(i in seq(along=expected)) expected[[i]] <- numeric(0)
expect_equal(genoprobs_col2drop(pr), expected)
expect_equal(genoprobs_col2drop(pr, FALSE), expected)
#####
# all males
fake.f2$is_female[fake.f2$is_female] <- FALSE
pr <- calc_genoprob(fake.f2)
# just X chromosome
expect_equal(genoprobs_col2drop(pr$X), 1:4)
# all chromosomes
expected$X <- 1:4
expect_equal(genoprobs_col2drop(pr), expected)
expect_equal(genoprobs_col2drop(pr, FALSE), expected)
# test Xonly=FALSE
expected2 <- expected;expected2$X <- numeric(0)
prA <- pr
attr(prA, "is_x_chr") <- rep(FALSE, length(prA))
expect_equal(genoprobs_col2drop(prA), expected2)
expect_equal(genoprobs_col2drop(prA, FALSE), expected)
#####
# all females
fake.f2$is_female[!fake.f2$is_female] <- TRUE
pr <- calc_genoprob(fake.f2)
# just X chromosome
expect_equal(genoprobs_col2drop(pr$X), 5:6)
# all chromosomes
expected$X <- 5:6
expect_equal(genoprobs_col2drop(pr), expected)
expect_equal(genoprobs_col2drop(pr, FALSE), expected)
# test Xonly=FALSE
expected2 <- expected;expected2$X <- numeric(0)
prA <- pr
attr(prA, "is_x_chr") <- rep(FALSE, length(prA))
expect_equal(genoprobs_col2drop(prA), expected2)
expect_equal(genoprobs_col2drop(prA, FALSE), expected)
})
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