tests/testthat/test-1-subset.R

In bigsnpr: Analysis of Massive SNP Arrays

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context("SUBSET")

test <- snp_attachExtdata()
# backing file
file <- test$genotypes$backingfile
# dimensions
n <- nrow(test$genotypes)
m <- ncol(test$genotypes)

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for (k in 1:10) {
  # taking only some individuals and some SNPs at random
  ind.row <- sort(sample(n, size = sample(50, 1)))
  ind.col <- sort(sample(m, size = sample(200, 1)))
  test2 <- snp_attach(subset(test, ind.row, ind.col))

  # classes
  test_that("good classes", {
    expect_s3_class(test2, "bigSNP")
    expect_s4_class(test2$genotypes, "FBM.code256")
    expect_s3_class(test2$fam, "data.frame")
    expect_s3_class(test2$map, "data.frame")
  })

  # dimensions
  test_that("Check new values", {
    expect_equal(test2$genotypes[], test$genotypes[ind.row, ind.col])
    expect_equivalent(test2$fam, test$fam[ind.row, ])
    expect_equivalent(test2$map, test$map[ind.col, ])
  })

  # new backing files
  test_that("backing files' names", {
    expect_equal(test2$genotypes$backingfile,
                 sub("\\.bk$", paste0("_sub", k, ".bk"), file))
  })
}

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# removing the 100th and 120th individuals
ind.row.del <- c(100, 120)
test3 <- snp_attach(subset(test, -ind.row.del))

# classes
test_that("good classes", {
  expect_s3_class(test3, "bigSNP")
  expect_s4_class(test3$genotypes, "FBM.code256")
  expect_s3_class(test3$fam, "data.frame")
  expect_s3_class(test3$map, "data.frame")
})

# dimensions
test_that("Check new values", {
  expect_equal(test3$genotypes[], test$genotypes[-ind.row.del, ])
  expect_equivalent(test3$fam, test$fam[-ind.row.del, ])
  expect_equivalent(test3$map, test$map)
})

# new backing files
test_that("backing files' names", {
  expect_equal(test3$genotypes$backingfile,
               normalizePath(sub("\\.bk$", paste0("_sub", k + 1, ".bk"), file)))
})

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test_that("Can subset without $fam or $map", {

  test4 <- test
  test4$fam <- NULL
  test5 <- snp_attach(snp_subset(test4, ind.col = 1:10))
  expect_null(test5$fam)
  expect_identical(test5$map, test$map[1:10, ])

  test6 <- test
  test6$map <- NULL
  test7 <- snp_attach(snp_subset(test6, ind.row = -(1:10)))
  expect_null(test7$map)
  expect_equal(test7$fam, test$fam[-(1:10), ], check.attributes = FALSE)
})

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