R/contrastPlot.bk.R

In kindlychung/CollapsABEL: An R package for quantitative CDH analysis

# contrastPlot_bk = function(hub,
#                         chrfilter=NULL,
#                         bplower=NULL,
#                         bpupper=NULL,
#                         bonferroni=FALSE,
#                         threshold=0.001,
#                         lowerPbonfer = FALSE,
#                         forceRecalc = TRUE
#                         ) {
# 
#     dat = cleanByChrPvalsBonfer(
#                                 hub = hub,
#                                 threshold = threshold,
#                                 sameChr = sameChr,
#                                 lowerPbonfer = lowerPbonfer,
#                                 forceRecalc = forceRecalc,
#                                 bpdiff = bpdiff
#                                 )
# 
#     # Take single-SNP data from hub, and QCDH data from dat
#     filter0 = rep(TRUE, nrow(hub$chr))
#     filter = rep(TRUE, nrow(dat))
#     if(! is.null(chrfilter)) {
#         filter0 = hub$chr[, 1] %in% chrfilter
#         filter = dat$chr %in% chrfilter
#     }
#     if(! is.null(bplower)) {
#         filter0 = filter0 & hub$bp[, 1] >= bplower
#         filter = filter & dat$bp >= bplower
#     }
#     if(! is.null(bpupper)) {
#         filter0 = filter0 & hub$bp[, 1] <= bpupper
#         filter = filter & dat$bp <= bpupper
#     }
#     if(! is.null(threshold)) {
#         filter0 = filter0 & hub$pvals[, 1] <= threshold
#         filter = filter & dat$p <= threshold
#     }
# 
#     filter0 = which(filter0)
#     filter = which(filter)
# 
#     chrvec0 = hub$chr[filter0, 1]
#     chrvec   = dat$chr[filter]
#     bpvec0 = hub$bp[filter0, 1]
#     bpvec    = dat$bp[filter]
# 
#     colorvec = c(rep("Single SNP", length(filter0)), rep("QCDH", length(filter)))
# 
#     basepvalsvec = hub$pvals[filter0, 1]
#     if(bonferroni) {
#         minpvalvec = dat$pbonfer[filter]
#     } else {
#         minpvalvec = dat$p[filter]
#     }
# 
#     chrvec = c(chrvec0, chrvec)
#     bpvec = c(bpvec0, bpvec)
#     pvalsvec = c(basepvalsvec, minpvalvec)
# 
#     posorder = order(chrvec, bpvec)
#     chrvec = chrvec[posorder]
#     bpvec = bpvec[posorder]
#     pvalsvec = pvalsvec[posorder]
#     colorvec = colorvec[posorder]
# 
#     resinfo = mqinfo(chr=chrvec, bp=bpvec, p=pvalsvec, colorvec=colorvec)
#     hub$contrastPlotOut = suppressWarnings(mh(resinfo))
#     hub$contrastPlotOut
# }