rARTP <- function(formula, data, pathway, family, geno.files = NULL, lambda = 1.0, subset = NULL, options = NULL){
options(warn = 1)
it <- input.type(geno.files)
if(it == 'data.frame'){
setup <- rawData.dataframe.setup(formula, data, pathway, family, lambda, subset, options)
}else{
if(it == 'geno.files'){
setup <- rawData.genofiles.setup(formula, data, pathway, family, geno.files, lambda, subset, options)
}else{
setup <- rawData.plinkfiles.setup(formula, data, pathway, family, geno.files, lambda, subset, options)
}
}
if(setup$options$only.setup){
return(setup)
}
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, deleted.snps = setup$deleted.snps,
deleted.genes = setup$deleted.genes,
options = setup$options, setup.timing = setup$setup.timing,
setup = setup)
}
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