# lambda is the second round adjusted inflation factor
# lambda is different with the ones in ARTP and sARTP, in which lambda is the study-specific first round inflation factor
warm.start <- function(setup, nperm = NULL, lambda = 1.0, nthread = NULL){
options(warn = 1)
setup <- validate.setup(setup)
setup <- update.setup(setup, nperm, lambda, nthread)
test <- norm.stat.test(setup)
options(warn = 0)
list(pathway.pvalue = test$pathway.pvalue, gene.pvalue = test$gene.pvalue,
model = test$model, most.sig.genes = test$most.sig.genes, arr.rank = test$arr.rank,
accurate = test$accurate, test.timing = test$test.timing,
pathway = setup$pathway, meta.stat = setup$meta.stat,
deleted.snps = setup$deleted.snps, deleted.genes = setup$deleted.genes,
options = setup$options, setup.timing = setup$setup.timing,
setup = setup)
}
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