Nothing
library(LoopRig)
# Load files
ovary_loops <- system.file("extdata/loops", "ovary_hg19.bedpe", package = "LoopRig", mustWork = TRUE)
ovary_loops_mcols <- system.file("extdata/loops", "ovary_hg19_mcol.bedpe", package = "LoopRig", mustWork = TRUE)
pancreas_loops <- system.file("extdata/loops", "pancreas_hg19.bedpe", package = "LoopRig", mustWork = TRUE)
spleen_loops <- system.file("extdata/loops", "spleen_hg19.bedpe", package = "LoopRig", mustWork = TRUE)
# Error handling
test_that("error handling", {
expect_error(LoopsToRanges(loop_names = NULL, custom_cols = 0, custom_mcols = NULL), "Please enter at least one BEDPE looping data file")
expect_error(LoopsToRanges(ovary_loops, ovary_loops), "Duplicate BEDPE data-files entered")
expect_error(LoopsToRanges(ovary_loops, pancreas_loops, custom_cols = 20), "Incorrect number of custom columns, please check your files again")
expect_error(LoopsToRanges(c("100", "200", "300"), ovary_loops), "Error in reading BEDPE files, please ensure file specification, format, and location accuracy")
expect_error(LoopsToRanges(pancreas_loops, ovary_loops, custom_mcols = 20), "Incorrect custom mcols location, please check your files again")
### Include chromosome coordinate check ###
})
# Expected class output
test_that("class output", {
expect_is(LoopsToRanges(ovary_loops, spleen_loops, custom_cols = 0), "LoopRanges")
expect_is(LoopsToRanges(ovary_loops_mcols, custom_cols = 1, custom_mcols = 7), "LoopRanges")
expect_is(LoopsToRanges(ovary_loops_mcols, custom_cols = 1, custom_mcols = 7, loop_names = "ovary_mcols"), "LoopRanges")
})
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