test_HmmGRanges.R
In VanillaICE: A Hidden Markov Model for high throughput genotyping arrays

## getOligoset <- function(){
## ##  path <- tryCatch(system.file("extdata", package="VanillaICE", mustWork=TRUE), error=function(e) NULL)
## ##  if(is.null(path)) path <- "~/Software/bridge/VanillaICE/inst/extdata"
## ##  load(file.path(path, "oligosetForUnitTest.rda"))
##   load("~/Software/bridge/man_VI/oligosetForUnitTest.rda")
##   se <- as(oligoset, "SnpArrayExperiment")
##   assays(se)[["cn"]] <- lrr(se)/100
##   baf(se) <- baf(se)/1000
##   saveRDS(se, file="~/Software/bridge/VanillaICE/inst/extdata/snp_exp.rds")
## }
##
## ##getSE <- function() {
## ##  se <- as(getOligoset(), "SnpArrayExperiment")
## ##
## ##  se
## ##}
##
## test_HmmGRanges <- function(){
##   library(oligoClasses)
##   library(IRanges)
##   path <- system.file("extdata", package="VanillaICE")
##   se <- readRDS(file.path(path, "snp_exp.rds"))
##   states <- Rle(factor(c(3, 4, 3, 5, 3, 2, 3, 3, 2, 3, 2, 3)),
##                 as.integer(c(996, 102, 902, 50, 2467, 102, 76, 1822,
##                              99, 900, 20, 160)))
##   hgr <- HmmGRanges(states=states,
##                     feature_starts=start(se),
##                     feature_chrom=chromosome(se),
##                     loglik=15.3)
##   checkTrue(validObject(hgr))
## }