tests/testthat/test-determine.input.R

In bedr: Genomic Region Processing using Tools Such as 'BEDTools', 'BEDOPS' and 'Tabix'

# The bedr package is copyright (c) 2014 Ontario Institute for Cancer Research (OICR)
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test_that('check that input format is correctly identified', {
	if (check.binary('tabix', verbose = TRUE)) {
		regions <- get.example.regions()
		region.a.bed.df1 <- index2bed(regions$a)
		region.a.bed.df2 <- index2bed(regions$a)
		colnames(region.a.bed.df2) <- c('a', 'b', 'c')
		region.a.index.df1 <- data.frame(index = regions$a, score = 1:length(regions$a), stringsAsFactors = FALSE)
		region.a.index.df2 <- data.frame(matrix(ncol = 3, nrow = length(regions$a)), row.names = regions$a, stringsAsFactors = FALSE)

		a <- bedr(engine = 'bedtools', input = list(i = regions$a), method = 'sort', params = '');
		b <- bedr(engine = 'bedtools', input = list(i = regions$b), method = 'sort', params = '');

		# index
		expect_equal(determine.input(a, verbose = FALSE), 0);

		# bed
		expect_equal(determine.input(region.a.bed.df1, verbose = FALSE), 1) # df with correct names
		expect_equal(determine.input(as.matrix(region.a.bed.df1), verbose = FALSE), 1) # matrix with correct names
		expect_equal(determine.input(region.a.bed.df2, verbose = FALSE), 1) # df with incorrect names

		# column index
		expect_equal(determine.input(region.a.index.df1, verbose = FALSE), 2);

		# row index 
		expect_equal(determine.input(region.a.index.df2, verbose = FALSE), 3);

		expect_equal(determine.input(as.matrix(region.a.bed.df2), verbose = FALSE), 4) # matrix with incorrect names fails due to string conversion
		expect_equal(determine.input(as.matrix(regions$a), verbose = FALSE), 4); # need to be more explicit
		expect_equal(determine.input(NA, verbose = FALSE), 4) # a vector but it doesn't look like an index
		}
	})