plotSampledPrev: Plotting expected

In Mangrove: Risk Prediction on Trees

Description

Two functions for plotting the expected distribution of affecteds in a family, either assuming no genetic risk factors, or using sampled from a custom distribution of affecteds (such as produced by MangroveTree).

Usage

plotNaivePrev(ped,K,maxN = NULL,...)
plotSampledPrev(samples, obs_prev, exp_prev, maxN = NULL, ...)

Arguments

ped	A MangrovePed object.
K	The prevalence of the disease.
samples	Samples from the distribution of number of affecteds.
obs_prev	The number of affecteds actually observed.
exp_prev	The expected number of affecteds under a naive model.
maxN	The maximum number of affecteds to be shown on the graph. If NULL, an appropriate maximum is selected from the data.
...	Additional arguments to plot.

Details

These functions are used to assess how "unusual" a family is in terms of the number of affected individuals it contains. plotNaivePrev plots the distribution of affected individuals in the family assuming no genetic risk factors (i.e. under a binomial model). plotSampledPrev is more general, and takes in a set of samples from the expected distribution.

Note that plotSampledPrev is called by plot.MangroveSample to plot the results of a MangroveTree sampling. It will be easier to use the print.MangroveSample method rather than using plotSampledPrev under most circumstances.

Value

Neither function returns anything.

See Also

MangroveSample

Examples

data(famped)

plotNaivePrev(famped,0.02) # is this unexpected for a 2% disease?
plotNaivePrev(famped,0.04) # how about for a 4% disease?

Mangrove documentation built on May 1, 2019, 9:10 p.m.