multiple.pathways.setup <- function(summary.files, pathway, family, reference, lambda,
ncases, ncontrols, nsamples, options){
start.time <- date()
# validate the format of main inputs
validate.summary.input(summary.files, pathway, family, reference, lambda,
ncases, ncontrols, nsamples)
# reformat reference to convert factor to character
reference <- reformat.reference.path(reference)
# merge and reset options
options <- options.setup(options, family, lambda, ncases, ncontrols, nsamples)
# load definition of pathway
pathway <- load.pathway.definition(pathway, options)
# load and check summary statistics
sum.stat <- load.summary.statistics(summary.files, pathway$SNP, options)
# estimate P and SE if they are not provided by users
sum.stat <- complete.sum.stat(sum.stat, options)$sum.stat
# split super-pathway into independent sub-pathways
sub.pathway <- create.sub.pathway(pathway)
# split summary statistics into sub-pathways
sum.stat <- split.sum.stat(sum.stat, sub.pathway)
# load SNPs and their reference and effect alleles in reference genotype
allele.info <- load.reference.allele(reference, pathway, options)
setup <- create.super.pathway.setup(sum.stat, allele.info, reference, sub.pathway, options)
setup
}
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