context("locus.R Diploid")
test_that("creating new ones", {
AB <- locus( c("A","B") )
loci <- c(AB,AB,AB)
locNULL <- locus()
expect_that( AB, is_a("locus") )
expect_that( nchar(locNULL), equals(0) )
expect_that(loci, is_a("locus"))
expect_that(length(loci), equals(3))
expect_that( loci[1], equals(AB))
})
test_that("passing NA", {
loc1 <- locus( NA )
expect_true( is.na(loc1))
loc2 <- locus( "NA:NA", type="separated")
expect_true( is.na(loc2))
})
test_that("List context",{
AB <- locus( c("A","B") )
loci <- c(AB,AB,AB)
lst <- as.list( loci )
expect_that( lst, is_a("list") )
expect_that( length(lst), equals(3) )
})
context("locus.R SNPs")
test_that("SNP Creation", {
loc.snp0 <- locus( 0, type="snp" )
loc.snp1 <- locus( 1, type="snp" )
loc.snp2 <- locus( 2, type="snp" )
loc.snp3 <- locus( 3, type="snp" )
expect_that( loc.snp0, is_a("locus") )
expect_that( loc.snp1, is_a("locus") )
expect_that( loc.snp2, is_a("locus") )
expect_that( loc.snp3, is_a("locus") )
loci <- locus( c(0,1,2), type="snp")
expect_that( loci, is_a("locus") )
expect_that( loci[1], equals( locus(c("A","A"))))
expect_that( loci[2], equals( locus(c("A","B"))))
expect_that( loci[3], equals( locus(c("B","B"))))
}
)
context("Locus.R columns ")
test_that( "Separated", {
x <- c( "A:B", "A:C", "B:C" )
loc <- locus( x, type="separated" )
expect_that( loc, is_a("locus"))
expect_that( length(loc), equals(3) )
expect_that( loc[1], equals( locus( c("A","B"))))
})
context("Locus.R separated ")
test_that( "Columns", {
twocol <- matrix( c(1,2,1,1,2,2), ncol=2, byrow=T)
loc <- locus( twocol, type="column" )
expect_that( loc, is_a("locus"))
expect_that( length(loc), equals(3) )
})
context( "Locus.R zyme-play")
test_that("testing",{
zyme <- c( "AA","AB","BB")
loc <- NULL
loc <- locus( zyme, type="zyme")
expect_that( loc, is_a("locus"))
expect_that( length(loc), equals(3) )
})
context("Locus.R operators")
test_that( "Operations", {
AA <- locus( c("A","A") )
AB <- locus( c("A","B") )
BB <- locus( c("B","B") )
AC <- locus( c("A","C") )
BC <- locus( c("B","C") )
expect_equal( AA, AA )
expect_false( AA==BB )
expect_true( AA!=AC )
expect_false( AA!=AA)
# addition operator
off <- AA+BB
expect_that( off, is_a("locus") )
expect_that( ploidy(off), equals(2) )
expect_true( is_heterozygote(off) )
expect_true( as.character(off)=="A:B" )
off <- AA-AA
expect_that( off, is_a("locus"))
expect_true( as.character(off)=="A" )
off <- AB-AB
expect_that( off, is_a("locus") )
expect_true( as.character(off)=="A:B")
off <- BB-AB
expect_true( as.character(off)=="B")
})
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