Nothing
test_that("HMM for haplotypes are loaded correctly", {
# Load HMM from RData
hmm.file <- system.file("extdata", "haplotypes_hmm.RData", package = "SNPknock")
load(hmm.file)
# Load fastPHASE parameter estimates from text files
r.file <- system.file("extdata", "haplotypes_rhat.txt", package = "SNPknock")
alpha.file <- system.file("extdata", "haplotypes_alphahat.txt", package = "SNPknock")
theta.file <- system.file("extdata", "haplotypes_thetahat.txt", package = "SNPknock")
char.file <- system.file("extdata", "haplotypes_origchars", package = "SNPknock")
hmm.compact <- loadHMM(r.file, alpha.file, theta.file, char.file)
hmm.large <- loadHMM(r.file, alpha.file, theta.file, char.file, compact=FALSE, phased=TRUE)
# Verify that the parameters are identical
testthat::expect_equal(hmm.hap$r, hmm.compact$r)
testthat::expect_equal(hmm.hap$alpha, hmm.compact$alpha)
testthat::expect_equal(hmm.hap$theta, hmm.compact$theta)
testthat::expect_equal(hmm.hap$pInit, hmm.large$pInit)
testthat::expect_equal(hmm.hap$Q, hmm.large$Q)
testthat::expect_equal(hmm.hap$pEmit, hmm.large$pEmit)
})
test_that("HMM for genotypes are loaded correctly", {
# Load HMM from RData
hmm.file <- system.file("extdata", "genotypes_hmm.RData", package = "SNPknock")
load(hmm.file)
# Load fastPHASE parameter estimates from text files
r.file <- system.file("extdata", "genotypes_rhat.txt", package = "SNPknock")
alpha.file <- system.file("extdata", "genotypes_alphahat.txt", package = "SNPknock")
theta.file <- system.file("extdata", "genotypes_thetahat.txt", package = "SNPknock")
char.file <- system.file("extdata", "genotypes_origchars", package = "SNPknock")
hmm.compact <- loadHMM(r.file, alpha.file, theta.file, char.file)
hmm.large <- loadHMM(r.file, alpha.file, theta.file, char.file, compact=FALSE, phased=FALSE)
hmm.large$Q <- hmm.large$Q[1:4,,]
hmm.large$pEmit <- hmm.large$pEmit[1:5,,]
# Verify that the parameters are identical
testthat::expect_equal(hmm.gen$r, hmm.compact$r)
testthat::expect_equal(hmm.gen$alpha, hmm.compact$alpha)
testthat::expect_equal(hmm.gen$theta, hmm.compact$theta)
testthat::expect_equal(hmm.gen$pInit, hmm.large$pInit)
testthat::expect_equal(hmm.gen$Q, hmm.large$Q)
testthat::expect_equal(hmm.gen$pEmit, hmm.large$pEmit)
})
test_that("Haplotypes are correctly converted into INP format", {
# Load haplotypes from RData and convert into INP
hap.file <- system.file("extdata", "haplotypes.RData", package = "SNPknock")
load(hap.file)
inp.file <- writeXtoInp(H, phased=T)
# Stored INP file
inp.file.stored <- system.file("extdata", "haplotypes.inp", package = "SNPknock")
testthat::expect_equal(readLines(inp.file), readLines(inp.file.stored))
})
test_that("Genotypes are correctly converted into INP format", {
# Load genotypes from RData and convert into INP
gen.file <- system.file("extdata", "genotypes.RData", package = "SNPknock")
load(gen.file)
inp.file <- writeXtoInp(X, phased=F)
# Stored INP file
inp.file.stored <- system.file("extdata", "genotypes.inp", package = "SNPknock")
testthat::expect_equal(readLines(inp.file), readLines(inp.file.stored))
})
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