tests/testthat/test_fraction.R

In AllelicImbalance: Investigates Allele Specific Expression

context("test fraction functionality")

#test_that(paste("test fraction default"), {
#
#	#prepare testdata
#	data(ASEset)	
#	x <- ASEset
#
#	res <- t(fraction(x))
#	res <- fraction(x)
#
#	#check 
#    expect_that(colnames(res), equals(rownames(x)))
#    expect_that(rownames(res), equals(colnames(x)))
#    expect_that(as.vector(res)[1:3], equals(c(0.8, 1.0, 1.0)))
#    expect_that(as.vector(res)[57:60], equals(c(NaN,1,1,1)))
#
#})
#
#
#test_that(paste("test fraction usePhase=TRUE"), {
#
#	#prepare testdata
#	#load data
#	data(ASEset) 
#    a <- ASEset
#  	                                                                                              
#	set.seed(1)
#    #example phase matrix 
#    p1 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
#    p2 <- matrix(sample(c(1,0),replace=TRUE, size=nrow(a)*ncol(a)),nrow=nrow(a), ncol(a))
#    pha <- matrix(paste(p1,sample(c("|","|","/"), size=nrow(a)*ncol(a), replace=TRUE), p2, sep=""),
#    	nrow=nrow(a), ncol(a))
#  	                                                                                              
#	#infer alt allele
#	mcols(a)[["alt"]] <- inferAltAllele(a)
#
#	#store
#	phase(a) <- pha
#	
#	#check 
#	res <- t(fraction(a, top.fraction.criteria="phase"))
#
#	#check 
#    expect_that(colnames(res), equals(rownames(a)))
#    expect_that(rownames(res), equals(colnames(a)))
#    expect_that(as.vector(res)[1:5], equals(c(0.2, 1.0, 1.0, 0.0, 1.0)))
#    expect_that(as.vector(res)[57:60], equals(c(NaN,0,0,0)))
#
#})
#
test_that(paste("checking .returnMaternalPhaseFrequency"), {

	#####################
	# Test 1 - 
	#####################
	
	#add one region that is missing
	ar <- aperm(array(c(T,T,F,F,F,F,F,F,F,F,F,T), dim=c(3,4,2)), c(1,3,2))
	fr <- array(c(0.3,0.2,0.3,0.2,0.8,0.2,0.3,0.7,0.4,0.2,0.1,0.3), dim=c(3,2,4))
	
	#prepare phase matrix
	ph <- array(c(1,1,0,0,1,0),dim=c(3,2))
	#prepare reference allele matrix
	rf <- array(c(0,0.2,0.8,0,0,1),dim=c(3,2))

	#prepeare expected data
	exp <- array(c(1.0,0.8,0.8,0,1,1), dim=c(3,2))

	#run tests
	res <- .returnMaternalPhaseFrequency(ph,rf)
	
	#test equality
    expect_equal(exp, res)


})