inst/unitTests/runit.impute2xxx_large.R

In GenABEL: genome-wide SNP association analysis

### --- Test setup ---

if(FALSE) {
	## Not really needed, but can be handy when writing tests
	library("RUnit")
	library("GenABEL")
}
#test.empty <- function(){}
### do not run
#stop("SKIP THIS TEST")
###

# common functions and data

data_prefix = "big_data/KOM"

### --- Test functions ---

test.impute2xxx_large <- function()
{
	
	unlink("*.fv?")
	unlink("tmp*")
	
	geno <- paste(data_prefix,".geno",sep="")
	info <- paste(data_prefix,".info",sep="")
	samp <- paste(data_prefix,".sample",sep="")
	
	if (!(file.exists(geno) && file.exists(info) && file.exists(samp))) {
		warning(paste("big files are missing; stopping tests"))
		return(NULL)
	}
	
	out <- "KOM_test_out.geno"
	fvdose <- impute2databel(geno=geno,
			sample=samp,
			out=out,
			makeprob=TRUE,
			old=FALSE)
	checkIdentical("databel",class(fvdose)[1])
	fvprob <- databel(paste(out,".prob",sep=""))
	checkIdentical("databel",class(fvprob)[1])
	checkIdentical(get_dimnames(fvdose)[[1]],get_dimnames(fvprob)[[1]])
	checkIdentical(dim(fvdose)[1],dim(fvprob)[1])
	prD2 <- (dim(fvprob)[2])/2
	checkEqualsNumeric(prD2,dim(fvdose)[2])
	
	rm(list=ls());gc()
	
	unlink("*.fv?")
	unlink("tmp*")
	
}