tests/testthat/test-AllUtilities.R

In PeteHaitch/MethylationTuples: Tools for analysing methylation patterns at genomic tuples

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### Tests of utility functions
###
context("Utility functions")

test_that(".makeMethPatNames works", {
  expect_identical(.makeMethPatNames(1), c('M', 'U'))
  expect_identical(.makeMethPatNames(2), c('MM', 'MU', 'UM', 'UU'))
  expect_identical(.makeMethPatNames(3), c('MMM', 'MMU', 'MUM', 'MUU', 
                                             'UMM', 'UMU', 'UUM', 'UUU'))
})

test_that(".validMethtype works", {
  
  expect_true(.validMethtype('CG'))
  expect_true(.validMethtype('CHG'))
  expect_true(.validMethtype('CHH'))
  expect_true(.validMethtype('CNN'))
  expect_true(.validMethtype(c('CG', 'CHG')))
  expect_true(.validMethtype(c('CG', 'CHH')))
  expect_true(.validMethtype(c('CG', 'CNN')))
  expect_true(.validMethtype(c('CHG', 'CHH')))
  expect_true(.validMethtype(c('CHG', 'CNN')))
  expect_true(.validMethtype(c('CHH', 'CNN')))
  expect_true(.validMethtype(c('CG', 'CHG', 'CHH')))
  expect_true(.validMethtype(c('CG', 'CHG', 'CNN')))
  expect_true(.validMethtype(c('CG', 'CHH', 'CNN')))
  expect_true(.validMethtype(c('CHG', 'CHH', 'CNN')))
  expect_true(.validMethtype(c('CG', 'CHG', 'CHH', 'CNN')))  
  expect_false(.validMethtype('CpG'))
  expect_false(.validMethtype('CG/CHG'))
})

test_that(".stranded works", {
  expect_true(.stranded(GRanges('1', IRanges(1:3, 1:3), strand = "+")))
  expect_true(.stranded(GRanges('1', IRanges(1:3, 1:3), strand = "-")))
  expect_false(.stranded(GRanges('1', IRanges(1:3, 1:3), strand = "*")))
  expect_true(.stranded(GRanges('1', IRanges(1:3, 1:3), 
                                strand = c("+", "-", "+"))))
  expect_false(.stranded(GRanges('1', IRanges(1:3, 1:3), 
                                 strand = c("+", "*", "+"))))
  expect_false(.stranded(GRanges('1', IRanges(1:3, 1:3), 
                                 strand = c("-", "*", "-"))))
  expect_false(.stranded(GRanges('1', IRanges(1:3, 1:3), 
                                 strand = c("+", "*", "-"))))
})