tests/testthat/test_gs3.R

In INRA/rgs3: R package wrapping the GS3 program for genomic selection

## Copyright 2016,2017 Institut National de la Recherche Agronomique (INRA)
##
## This file is part of rgs3.
##
## rgs3 is free software: you can redistribute it and/or modify
## it under the terms of the GNU General Public License as
## published by the Free Software Foundation, either version 3 of the
## License, or (at your option) any later version.
##
## rgs3 is distributed in the hope that it will be useful,
## but WITHOUT ANY WARRANTY; without even the implied warranty of
## MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
## GNU General Public License for more details.
##
## You should have received a copy of the GNU General Public
## License along with rgs3.  If not, see
## <http://www.gnu.org/licenses/>.

library(rgs3)
context("Gs3")

test_that("writeDataForGs3", {
  tmpd <- tempdir()

  phenos <- data.frame(geno=paste0("geno", 1:3),
                       trait.cont=c(0.24, 1.17, NA),
                       trait.bin=c(1, NA, 0))
  phenos.file <- paste0(tmpd, "/phenos.txt")
  inds <- setNames(object=1:3, nm=paste0("geno", 1:3))

  expected <- as.data.frame(matrix(c(1:3,
                                     c(0.24, 1.17, -9999),
                                     c(1, 0, 0)),
                                   nrow=3, ncol=3))

  writeDataForGs3(x=phenos,
                  file=phenos.file,
                  inds=inds,
                  col.id=1,
                  col.traits=c(2,3),
                  binary.traits=c(FALSE,TRUE))

  observed <- read.table(file=phenos.file)

  expect_equal(observed, expected)

  if(file.exists(phenos.file))
    file.remove(phenos.file)
})

test_that("getPartitionGenos_equal", {
  geno.names <- paste0("geno", 1:4)
  expected <- setNames(object=c(1, 1, 2, 2), nm=geno.names)
  observed <- getPartitionGenos(geno.names=geno.names,
                                nb.folds=2,
                                seed=NULL)
  expect_equal(observed, expected)
})

test_that("getPartitionGenos_unequal", {
  geno.names <- paste0("geno", 1:5)
  expected <- setNames(object=c(1, 1, 1, 2, 2), nm=geno.names)
  observed <- getPartitionGenos(geno.names=geno.names,
                                nb.folds=2,
                                seed=NULL)
  expect_equal(observed, expected)
})