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##### Function to generate data for exploratory plots #####
# By Sonia & Pedro
# Modified: 2-jun-15
dat = function (input, type = c("biodetection","cd","countsbio","GCbias","lengthbias","saturation","PCA"),
k = 0, ndepth = 6, factor = NULL, norm = FALSE, refColumn = 1, logtransf = FALSE) {
type <- match.arg(type)
if (type == "biodetection") {
output = new("Biodetection", dat = biodetection.dat(input, factor = factor, k = k))
}
if (type == "cd") {
output = new("CD", dat = cd.dat(input, norm = norm, refColumn = refColumn))
}
if (type == "countsbio") {
output = new("CountsBio", dat = countsbio.dat(input, factor = factor, norm = norm))
}
if (type == "GCbias") {
output = new("GCbias", dat = GC.dat(input, factor = factor, norm = norm))
}
if (type == "lengthbias") {
output = new("lengthbias", dat = length.dat(input, factor = factor, norm = norm))
}
if (type == "saturation") {
output = new("Saturation", dat = saturation.dat(input, k = k, ndepth = ndepth))
}
if (type == "PCA") {
output = new("PCA", dat = PCA.dat(input, norm = norm, logtransf = logtransf))
}
output
}
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