R/updateMinPvals.R

In kindlychung/collr2: QCDH

updateMinPvals = function(hub, bpdiff=5e5) {
    pvals_tmp = hub$pvals
    # don't use those p values with BP distance too big
    pvals_tmp[abs(hub$bp2 - hub$bp) > bpdiff] = NA
    # don't use those p value where SNP pair are from different chromosomes
    pvals_tmp[hub$chr != hub$chr2] = NA
    
    hub$minPvals = do.call(pminNoNA, as.data.frame(pvals_tmp))
    hub$ntests = apply(hub$pvals, 1, function(rowIter) {sum(!is.na(rowIter))})
    hub$minPvalsBonfer = hub$minPvals * hub$ntests
    hub$minPvalsBonfer = ifelse(hub$minPvalsBonfer > 1, 1, hub$minPvalsBonfer)
    invisible(NULL)
}