FamEvent (version 2.1)

plot.penmodel: Plot method for penmodel

Description

Plots penetrance curves estimated from the fitted penetrance model and overlays non-parametric penetrance curves estimated from the data without proabands.

Usage

# S3 method for penmodel
plot(x, agemax = 80, print = TRUE, mark.time = FALSE, conf.int = FALSE, 
add.KM = TRUE, MC = 100, col = c("blue", "red", "blue", "red"), lty = c(1, 1, 2, 2), 
add.legend = TRUE, add.title = TRUE, xpos = "topleft", ypos = NULL, 
xlab = "Age at onset", ylab = "Penetrance", ylim = NULL, main = NULL,  ...)

Arguments

x

An object class of 'penmodel', a fitted model by penmodel or penmodelEM functions.

agemax

Maximum age of disease onset or maximum age. Default is 80 years of age.

print

Logical; if TRUE, displays parameter estimates and penetrance estimates by age 70.

mark.time

Logical; if TRUE, curves are marked at each censoring time, otherwise, no labeling is done.

conf.int

Logical; if TRUE, displays 95% confidence intervals for both parametric and non-parametric penetrance estimates for each subgroup and returns their lower and upper limits.

add.KM

Logical; if TRUE, displays Kaplan-Meier curves from data.

MC

Number of simulated samples used to calculate confidence intervals with a Monte-Carlo method. If MC = 0, no confidence intervals will be calculated. Default value is 100.

col

Colors of lines for male carriers, female carriers, male noncarrers, and female noncarriers. Default is c("blue", "red", "blue", "red").

lty

Types of lines for male carriers, female carriers, male noncarriers, and female noncarriers. Default is c(1, 1, 2, 2).

add.legend

Logical; if TRUE, displays a legend in the plot.

add.title

Logical; if TRUE, displays a title in the plot.

xpos, ypos

Position of legend; see legend. Defaults are xpos = "topleft", ypos = NULL.

xlab

Title for the x-axis. Default is "Age at onset".

ylab

Title for the y-axis. Default is "Penetrance".

ylim

Limits for the y-axis. Default is NULL. If NULL, ylim will be automatically determined.

main

Main title of the plot. Default is NULL. If NULL, the title will be automatically created.

...

Other parameters to be passed through to plotting functions.

Value

Returns the following summary values:

coefficients

Parameter estimates of transformed baseline parameters (\(\lambda, \rho\)) and regression coefficients for gender and mutation status (\(\beta_s, \beta_g\)).

pen70

Penetrance estimates by age 70, specific to gender and mutation-status subgroups.

x.age

Vector of ages of onsest ranging from agemin to agemax years

pen

Penetrance estimates at each age in x.age, specific to gender and mutation-status subgroups.

lower

Lower limits of 95% confidence interval estimates for penetrance at each age in x.age, specific to gender and mutation status subgroups.

upper

Upper limits of 95% confidence interval estimates for penetrance at each age in x.age, specific to gender and mutation status subgroups.

Details

The 95% confidence intervals for the parametric penetrance curves are obtained based on simulations of the parameters, assuming a multivariate normal distribution for the estimated parameters with their variance-covariance matrix. See penetrance for more details.

See Also

penmodel, print.penmodel, penmodelEM, summary.penmodel,print.summary.penmodel, simfam

Examples

# NOT RUN {
# Simulated family data  

set.seed(4321)
fam <- simfam(N.fam = 300, design = "pop+", base.dist = "Weibull", variation = "none",
       base.parms = c(0.01,3), vbeta = c(-1.13, 2.35), allelefreq = 0.02, agemin = 20)
 
# Fit family data

fit <- penmodel(Surv(time, status) ~ gender + mgene, cluster = "famID", design = "pop+",
parms = c(0.01, 3, -1.13, 2.35), data = fam, base.dist = "Weibull", robust = TRUE)       

# Plot penetrance function curves with 95% CIs

plot(fit, agemax = 80, conf.int = TRUE)

# }