Nothing
test_that("bdapply", {
vcf1abdfile <- system.file("extdata", "set1a.vcf", package = "BinaryDosage")
vcfinfo <- getvcfinfo(vcffiles = vcf1abdfile,
index = FALSE)
vcf1abdfile <- system.file("extdata", "vcf1a.bdose", package = "BinaryDosage")
expect_error(bdinfo <- getbdinfo(bdfiles = vcf1abdfile), NA)
func <- getaaf
aaf1afile <- system.file("extdata", "aaf1a.rds", package = "BinaryDosage")
aaf1a <- readRDS(aaf1afile)
expect_error(bdapply(),
"No binary dosage file information specified")
expect_error(bdapply(bdinfo = 1,
func = func),
"bdinfo does not contain information about a binary dosage file")
expect_error(bdapply(bdinfo = vcfinfo,
func = func),
"bdinfo does not contain information about a binary dosage file")
expect_error(bdapply(bdinfo = bdinfo),
"No function specified")
expect_error(bdapply(bdinfo = bdinfo, func = 1),
"func is not a function")
expect_equal(unlist(bdapply(bdinfo = bdinfo,
func = func)),
aaf1a,
tolerance = 4e-5)
})
test_that("vcfapply", {
vcf1abdfile <- system.file("extdata", "set1a.vcf", package = "BinaryDosage")
vcfinfo <- getvcfinfo(vcffiles = vcf1abdfile)
vcf1abdfile <- system.file("extdata", "vcf1a.bdose", package = "BinaryDosage")
bdinfo <- getbdinfo(bdfiles = vcf1abdfile)
func <- getaaf
aaf1afile <- system.file("extdata", "aaf1a.rds", package = "BinaryDosage")
aaf1a <- readRDS(aaf1afile)
expect_error(vcfapply(),
"No vcf file information specified")
expect_error(vcfapply(vcfinfo = 1,
func = func),
"vcfinfo does not appear to contain information about a vcf file")
expect_error(vcfapply(vcfinfo = bdinfo,
func = func),
"vcfinfo does not appear to contain information about a vcf file")
expect_error(vcfapply(vcfinfo = vcfinfo),
"No function specified")
expect_error(vcfapply(vcfinfo = vcfinfo, func = 1),
"func is not a function")
expect_equal(unlist(vcfapply(vcfinfo = vcfinfo,
func = func)),
aaf1a,
tolerance = 4e-5)
vcf1andfile <- system.file("extdata", "set1a_nd.vcf.gz", package = "BinaryDosage")
expect_error(vcfinfo <- getvcfinfo(vcf1andfile,
gz = TRUE,
index = FALSE),
NA)
expect_equal(unlist(vcfapply(vcfinfo = vcfinfo,
func = getaaf)),
aaf1a,
tolerance = 4e-5)
})
test_that("genapply", {
gen1afile <- system.file("extdata", "set1a.imp", package = "BinaryDosage")
geninfo <- getgeninfo(genfiles = gen1afile,
snpcolumns = c(1L, 3L, 2L, 4L, 5L),
header = TRUE)
vcf1abdfile <- system.file("extdata", "vcf1a.bdose", package = "BinaryDosage")
bdinfo <- getbdinfo(bdfiles = vcf1abdfile)
func <- getaaf
aaf1afile <- system.file("extdata", "aaf1a.rds", package = "BinaryDosage")
aaf1a <- readRDS(aaf1afile)
expect_error(genapply(),
"No gen file information specified")
expect_error(genapply(geninfo = 1,
func = func),
"geninfo does not appear to contain information about a gen file")
expect_error(genapply(geninfo = bdinfo,
func = func),
"geninfo does not appear to contain information about a gen file")
expect_error(genapply(geninfo = geninfo),
"No function specified")
expect_error(genapply(geninfo = geninfo, func = 1),
"func is not a function")
expect_equal(unlist(genapply(geninfo = geninfo,
func = func)),
aaf1a,
tolerance = 4e-5)
gen4afile <- system.file("extdata", "set4a.imp.gz", package = "BinaryDosage")
gen4asample <- system.file("extdata", "set4a.sample", package = "BinaryDosage")
expect_error(geninfo <- getgeninfo(genfiles = c(gen4afile, gen4asample),
snpcolumns = c(1L, 2L, 4L:6L),
startcolumn = 7L,
impformat = 2L,
gz = TRUE,
index = FALSE),
NA)
expect_equal(unlist(genapply(geninfo = geninfo,
func = func)),
aaf1a,
tolerance = 4e-5)
})
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