plot.penmodel: Plot method for 'penmodel'

In FamEvent: Family Age-at-Onset Data Simulation and Penetrance Estimation

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 class '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.

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.

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.

Author(s)

Yun-Hee Choi

See Also

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

Examples

# 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)

FamEvent documentation built on May 29, 2024, 6:22 a.m.