DNAmixturesLite (version 0.0-1)

qqpeak: Quantile-Quantile plot for assessing the distribution of observed peak heights.

Description

Given \(Z_a \ge C\), the peak height \(Z_a\) follows a continuous distribution. The probability transform \(P(Z_a \le z_a| Z_a \ge C)\) thus follows a uniform distribution. The function qqpeak computes the quantiles of the probability transform and produces a quantile-quantile plot. Information about the other peak heights in the EPG may be taken into account in the distribution of a peak.

IMPORTANT: This is the DNAmixturesLite package, which is intended as a service to enable users to try DNAmixtures without purchasing a commercial licence for Hugin. When at all possible, we strongly recommend the use of DNAmixtures rather than this lite-version. See https://dnamixtures.r-forge.r-project.org/ for details on both packages.

While the lite-version seeks to provide the full functionality of DNAmixtures, note that computations are much less efficient and that there are some differences in available functionality. Be aware that the present documentation is copied from DNAmixtures and thus may not accurately describe the implementation of this lite-version.

Usage

qqpeak(
  x,
  pars,
  dist = c("joint", "conditional", "prequential"),
  by.allele = TRUE,
  plot = TRUE,
  xlab = "Uniform quantiles",
  ylab = NULL,
  xlim = NULL,
  ylim = xlim,
  ...
)

Value

A data.frame containg quantiles q

corresponding to \(P(Z < z_{obs} | Z > 0)\) in the specified distribution, together with other quantities computed by predict.DNAmixture. The data are ordered according to q.

Arguments

x

A DNAmixture model.

pars

A mixpar parameter.

dist

"joint", "conditional", or "prequential". See predict.DNAmixture for details.

by.allele

Order of conditioning when dist="prequential". See predict.DNAmixture

plot

Should a plot be produced? Defaults to TRUE.

xlab

Legend for the x-axis.

ylab

Legend for y-axis.

xlim

Range of x-axis. Default is a plot with equal ranges on the x- and y-axis.

ylim

Range of y-axis.

...

Other arguments to be passed on to plot.

Author

Therese Graversen

Examples

data(MC15, MC18, USCaucasian)
mix <- DNAmixture(list(MC15, MC18), C = list(50, 38), k = 3, K = c("K1", "K3"),
                  database = USCaucasian)
p <- mixpar(rho = list(30, 30), eta = list(30, 30), xi = list(0.08,0.08),
            phi = list(c(U1 = 0.1, K3 = 0.2, K1 = 0.7)))
qqpeak(mix, pars = p, dist = "conditional")
# \donttest{
## If desired, we can make a customised plot -- here we color according to the two mixtures
qq <- qqpeak(mix, pars = p, dist = "conditional", plot = FALSE)
plot(ppoints(qq$q), qq$q, xlab = "Uniform quantiles", ylab = "Probability transform",
     col = qq$trace, pch = qq$trace)
# }