inst/unitTests/test_FamilyExperiment.R

In syounkin/Trioconductor: Trioconductor

test_PedClass <- function(){
	checkTrue(validObject(PedClass()))
	data(sample)
	checkTrue(validObject(PedClass(ped.DF)))
	## must have all the required columns
	checkException(validObject(PedClass(DataFrame(mid="a"))))
}

##test_FamilyExperiment <- function(){
##	checkTrue(validObject(FamilyExperiment))
##}

## make_test_Pedigree <- function(){
## 	pedTest <- new("Pedigree", trios=data.frame(F=c("NA06993", "NA11881"),
## 				   M=c("NA06985", "NA11882"),
## 				   O=c("NA06991", "NA10859"),
## 				   stringsAsFactors=FALSE),
## 		       trioIndex=data.frame(individualId=c("NA06993", "NA11881",
## 				   "NA06985", "NA11882", "NA06991", "NA10859"),
## 		       memberId=rep(c("F", "M", "O"), each=2),
## 		       index.in.pedigree=rep(1:2, 3),
## 		       stringsAsFactors=FALSE))
## }

## test_Pedigree_construction <- function(){
## 	library(oligoClasses)
## 	checkTrue(validObject(Pedigree()))
## 	path <- system.file("extdata", package="MinimumDistance")
## 	load(file.path(path, "pedigreeInfo.rda"))
## 	ped <- Pedigree(fatherIds=pedigreeInfo$F,
## 			motherIds=pedigreeInfo$M,
## 			offspringIds=pedigreeInfo$O)
## 	checkTrue(validObject(ped))

## 	ped2 <- ped[2, ]
## 	checkTrue(validObject(ped2))
## 	checkTrue(validObject(Pedigree(pedigreeInfo)))

## 	##validObject(ped[1, ])
## 	ped2 <- make_test_Pedigree()
## 	checkIdentical(ped, ped2)

## 	## can not have duplicate offspring identifiers
## 	checkException(Pedigree(data.frame(F=c("F0.txt", "F0.txt"),
## 					   M=c("M0.txt", "M0.txt"),
## 					   O=c("O0.txt", "O0.txt"))), silent=TRUE)

## 	checkTrue(validObject(Pedigree(data.frame(F=c("F0.txt", "F0.txt"),
## 						  M=c("M0.txt", "M0.txt"),
## 						  O=c("O0.txt", "O1.txt")))))

## 	trio <- trios(ped)
## 	trio$F[[1]] <- "badname"
## 	ped@trios <- trio
## 	checkException(validObject(ped), silent=TRUE)

## 	checkTrue(identical(sampleNames(ped), offspringNames(ped)))
## }

## test_subsetPedigree <- function(){
## 	object <- Pedigree(fatherIds=rep(letters[1:3], each=2),
## 			   motherIds=rep(letters[4:6], each=2),
## 			   offspringIds=letters[11:16])
## 	checkTrue(validObject(object[6, ]))
## 	## offspring is both parent and an offspring in the same trio
## 	## (should throw an error)
## 	checkException(Pedigree(fatherIds=rep(letters[1:2]),
## 				motherIds=rep(letters[3:4]),
## 				offspringIds=letters[c(1,5)]))
## 	## offspring is a parent in one trio and an offspring in a
## 	## different trio (should be valid)
## 	ped <- Pedigree(fatherIds=rep(letters[1:2]),
## 			motherIds=rep(letters[3:4]),
## 			offspringIds=letters[c(5,1)])
## 	checkTrue(validObject(ped))

## 	validObject(Pedigree(data.frame(F=letters[1],
## 					M=letters[2],
## 					O=letters[3])))
## }