Nothing
library(testthat)
library(detectRUNS)
context("Testing RUNS")
# get file paths: reference file need to be changed or removed
genotypeFile <- "test.ped"
mapFile <- "test.map"
test_that("detected ROHet are identical", {
# testing slinding windows
test_sliding <- slidingRUNS.run(genotypeFile, mapFile, windowSize=15, threshold=0.1, minSNP=15,
ROHet=FALSE, maxOppWindow=1, maxMissWindow=1, minLengthBps=100000,
minDensity=1/10000, maxOppRun=NULL, maxMissRun=NULL)
# reading rohet reference: this need to be updated
colClasses <- c(rep("character", 3), rep("numeric", 4) )
reference_rohet <- read.csv2("test.ROHet.sliding.csv", header = T, stringsAsFactors = FALSE, colClasses = colClasses)
# compare rohet table
expect_equal(test_sliding, reference_rohet, info = "testing sliding window approach")
# testing slinding windows
test_consecutive <- consecutiveRUNS.run(genotypeFile, mapFile, minSNP=15,
ROHet=FALSE, minLengthBps=100000,
maxOppRun=1, maxMissRun=1)
# reading rohet reference: this need to be updated
colClasses <- c(rep("character", 3), rep("numeric", 4) )
reference_rohet <- read.csv2("test.ROHet.consecutive.csv", header = T, stringsAsFactors = FALSE, colClasses = colClasses)
# compare rohet table
expect_equal(test_consecutive, reference_rohet, info = "testing consecutive approach")
})
test_that("Marker differ in size", {
# read mapFile
mapFile <- read.delim(mapFile, header = F)
names(mapFile) <- c("Chrom","SNP","cM","bps")
# subset mapfile
mapFile <- mapFile[100, ]
# write a fake mapfile in a temporary dir
fake_mapfile = tempfile(fileext = ".map")
write.table(mapFile, fake_mapfile, quote = FALSE, sep = "\t", row.names = FALSE, col.names = FALSE)
# test function
expect_error(slidingRUNS.run(genotypeFile, fake_mapfile), "Number of markers differ")
# clean up
file.remove(fake_mapfile)
})
test_that("No file path throws error", {
# test for errors
expect_error(slidingRUNS.run("fake_genotype", mapFile), "doesn't exists")
expect_error(slidingRUNS.run(genotypeFile, "fake_map"), "doesn't exists")
})
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