context("Qualvar tests")
# test that file read capability of Qualvar
qualvar=data.frame("V1"=c(rep("GENE1",5),rep("GENE2",6)),
"V2"=c(rep("1-100-A-C",2), "1-105-C-T",
rep("1-110-G-C",2), "2-100-A-C",
"2-106-C-T", rep("2-111-G-A",3),
"2-112-G-T"),
"V3"=c("sample1","sample3","ctrl1","sample5",
"sample8","ctrl6","ctrl4","sample5",
"sample6","sample8","ctrl2"),
"V4"=c(rep(1,9),2,1),
stringsAsFactors=F, check.names=F)
test_that("Qualvar read function works properly", {
qualvar.test <- QualvarRead("famctrl.qualvar")
expect_equal(qualvar, qualvar.test)
})
# test sample / geneset subsetting capability of Qualvar
qualvar.casectrl<-data.frame("V1"=c(rep("GENE1",3),rep("GENE2",4)),
"V2"=c(rep("1-100-A-C",1), "1-105-C-T",
rep("1-110-G-C",1), "2-100-A-C",
"2-106-C-T", rep("2-111-G-A",1),
"2-112-G-T"),
"V3"=c("sample1","ctrl1","sample5",
"ctrl6","ctrl4","sample5",
"ctrl2"),
"V4"=c(rep(1,7)),
stringsAsFactors=F, check.names=F)
test_that("Qualvar subsetting is working properly", {
qualvar.test <- QualvarRead("famctrl.qualvar",
samples=c("sample1","sample5","ctrl1",
"ctrl2","ctrl3",
"ctrl4","ctrl5","ctrl6"),
geneset=c("GENE1","GENE2","GENE3") )
rownames(qualvar.casectrl) <- NULL
rownames(qualvar.test) <- NULL
expect_equal(qualvar.casectrl, qualvar.test)
})
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