inst/unitTests/test_splitsForCBS.R

In rscharpf/MinimumDistance: A Package for De Novo CNV Detection in Case-Parent Trios

test_cbsSplits <- function(){
##	require("human610quadv1bCrlmm")
##	library(oligoClasses)
##	library2(foreach)
##	path <- system.file("extdata", package="human610quadv1bCrlmm")
##	load(file.path(path, "snpProbes_hg18.rda"))
##	load(file.path(path, "cnProbes_hg18.rda"))
##	x <- matrix(NA, nrow=nrow(snpProbes)+nrow(cnProbes), 1)
##	rownames(x) <- c(rownames(snpProbes), rownames(cnProbes))
##	fd <- GenomeAnnotatedDataFrameFrom(x, annotationPkg="human610quadv1bCrlmm", genome="hg18")
##	fd <- fd[order(chromosome(fd), position(fd)), ]
##	fd <- fd[chromosome(fd) < 23, ]
##	pos <- position(fd)
##	index <- split(seq_len(nrow(fd)), chromosome(fd))
##	res <- foreach(i=index) %do% MinimumDistance:::splitByDistance(pos[i], 100e3)
##	tabs <- lapply(res, table)
##	checkTrue(all(unlist(tabs) > 1000))
}