## this can be slow
library(oligoClasses)
if (require(genomewidesnp6Crlmm) & require(hapmapsnp6)){
path <- system.file("celFiles", package="hapmapsnp6")
## the filenames with full path...
## very useful when genotyping samples not in the working directory
cels <- list.celfiles(path, full.names=TRUE)
(crlmmOutput <- crlmm(cels))
## If gender is known, one should check that the assigned gender is
## correct, or pass the integer coding of gender as an argument to the
## crlmm function as done below
}
## Not run:
# ## HPC Example
# library(ff)
# library(snow)
# library(crlmm)
# ## genotype 50K SNPs at a time
# ocProbesets(50000)
# ## setup cluster - 8 cores on the machine
# library(doSNOW)
# cl <- makeCluster(8, "SOCK")
# registerDoSNOW(cl)
# ##setCluster(8, "SOCK")
#
# path <- system.file("celFiles", package="hapmapsnp6")
# cels <- list.celfiles(path, full.names=TRUE)
# crlmmOutput <- crlmm2(cels)
# ## End(Not run)
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