summary.penmodel: Summary method for class 'penmodel'

Description Usage Arguments Value Author(s) See Also Examples

Description

Provides a summary of a fitted penetrance model.

Usage

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## S3 method for class 'penmodel'
summary(object, correlation=FALSE, ...)

Arguments

object

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

correlation

Logical; if TRUE, returns the correlation matrix of the estimated parameters.

...

Further arguments passed to or from other methods.

Value

Returns the object of class 'summary.penmodel', including the following summary values:

coefficients

4 x 4 matrix with columns for parameter estimates of transformed baseline parameters (λ, ρ) and regression coefficients for gender and mutation status (β_s, β_g), their standard errors (or robust standard errors if robust=TRUE was selected when fitting the penetrance model), t-statistics and corresponding two-sided p-values.

varcov

4 x 4 variance covariance matrix of the parameter estimates.

correlation

Correlation matrix corresponding to the specified variance covariance matrix, if correlation=TRUE is specified.

pen70

Penetrance estimates by age 70 specific to gender and mutation-status subgroups including their standard errors and 95% confidence intervals.

Author(s)

Yun-Hee Choi

See Also

penmodel, penmodelEM, print.penmodel, print.summary.penmodel plot.penmodel

Function coef will extract the matrix of coefficients with standard errors, t-statistics and p-values.

Examples

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# Simulated family data 

fam <- simfam(N.fam=300, design="pop+", variation="none", base.dist="Weibull", 
       base.parms=c(0.01,3), vbeta=c(-1.13, 2.35), agemin=20, allelefreq=0.02)
 
# Penetrance model fit for the simulated family data

fit <- penmodel(parms=c(0.01, 3), vbeta=c(-1.13, 2.35), data=fam, 
       design="pop+", base.dist="Weibull")

# Summary of the model parameter and penetrance estimates from model fit

summary(fit)

## Not run: 
Coefficients: 
            Estimate Std. Error t value Pr(>|t|)  
log(lambda)   -4.637    0.07989 -58.048  0.01097 *
log(rho)       1.094    0.03910  27.980  0.02274 *
beta.sex      -1.315    0.16298  -8.066  0.07852 .
beta.gene      2.545    0.21423  11.881  0.05346 .
Signif. codes:   0 '***'  0.001 '**' 0.01 '*' 0.05 '.' 0.1 ' ' 1 

Penetrance (%) by age 70: 
         Male Carrier Female Carrier Male Noncarrier Female Noncarrier
Estimate        32.47          76.82            3.03             10.83
SE               3.85           3.22            0.74              2.17

95% Confidence intervals on the penetrances: 
           Male Carrier Female Carrier Male Noncarrier Female Noncarrier
lowerlimit        25.59          70.43            1.94              7.43
upperlimit        40.70          83.08            4.85             15.87

## End(Not run)


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