plot.penmodel function

Plot method for penmodel

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

## 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.

Returns

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)