basePlot = function(hub, chrfilter=NULL, bplower=NULL, bpupper=NULL, pvallower=NULL, pvalupper=NULL) {
filter = rep(TRUE, hub$nsnp)
filtered = FALSE
if(! is.null(chrfilter)) {
#debugps(paste("Filtering by chromosome, as you requested..."))
filter = hub$chr[, 1] %in% chrfilter
filtered = TRUE
}
if(! is.null(bplower)) {
#debugps(paste("Filtering by bp lower limit, as you requested..."))
filter = filter & hub$bp[, 1] >= bplower
filtered = TRUE
}
if(! is.null(bpupper)) {
#debugps(paste("Filtering by bp upper limit, as you requested..."))
filter = filter & hub$ bp[, 1] <= bpupper
filtered = TRUE
}
if(! is.null(pvallower)) {
#debugps(paste("Filtering by pval lower limit, as you requested..."))
filter = filter & hub$pvals[, 1] > pvallower
filtered = TRUE
}
if(! is.null(pvalupper)) {
#debugps(paste("Filtering by pval upper limit, as you requested..."))
filter = filter & hub$pvals[, 1] < pvalupper
filtered = TRUE
}
if(filtered) {
filter = which(filter)
chrvec = hub$chr[filter, "0000"]
bpvec = hub$bp[filter, "0000"]
pvalsvec = hub$pvals[filter, "0000"]
} else {
chrvec = hub$chr[, "0000"]
bpvec = hub$bp[, "0000"]
pvalsvec = hub$pvals[, "0000"]
}
resinfo = mqinfo(chr=chrvec, bp=bpvec, p=pvalsvec)
suppressWarnings(mh(resinfo))
}
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