R/minPCom.R

In diptavo/MultiSKAT: Sequence Kernel Association Tests with Multiple phenotypes

minPcom <- function(obj.res,Sigma_Ps,Z,resample = 200,weights.beta=c(1,25), kernel = "linear.weighted", Is.Common=FALSE,  weights = NULL
                            , impute.method = "fixed",   is_check_genotype=TRUE, is_dosage = FALSE, missing_cutoff=0.15, estimate_MAF=1,max_maf = 1,verbose = TRUE){

	if(class(obj.res) == "MultiSKAT_NULL_unrelated"){
		re <- minPcom_base(obj.res,Sigma_Ps,Z,resample = resample,kernel = kernel, Is.Common=Is.Common, weights.beta=weights.beta, weights = weights, impute.method = impute.method,   is_check_genotype=is_check_genotype, is_dosage = is_dosage, missing_cutoff=missing_cutoff, estimate_MAF=estimate_MAF,max_maf=max_maf,verbose = verbose)}
	else{
		re <- minPcom_Kins(obj.res,Sigma_Ps,Z,resample = resample,kernel = kernel, Is.Common=Is.Common, weights.beta=weights.beta, weights = weights, impute.method = impute.method, is_check_genotype=is_check_genotype, is_dosage = is_dosage, missing_cutoff=missing_cutoff, estimate_MAF=estimate_MAF,max_maf=max_maf,verbose = verbose)}
	return(re)
}