kc.moments {kin.cohort}R Documentation

Kin-cohort estimation of penetrance by the method of moments

Description

This function estimates cumulative risk and hazard at given ages for carriers and noncarriers of a mutation based on the probands genotypes. It uses the method of moments described by Wacholder et al (1998)

Usage

kc.moments(t, delta, genes, r, knots, f, pw = rep(1,length(t)), 
           set = NULL, B = 1, logrank = TRUE, subset, trace=FALSE)

Arguments

t time variable. Usually age at diagnosis or at last follow-up
delta disease status (1: event, 0: no event
genes genotype of proband numeric. A factor is preferred, otherwise numeric code of genotypes (1: noncarrier, 2:carrier, [3: homozygous carrier])
r relationship with proband 1:parent, 2:sibling 3:offspring 0:proband. Probands will be excluded from analysis and offspring will be recoded 1 internally.
knots time points (ages) for cumulative risk and hazard estimates
f mutation allele frequency in the population
pw prior weights, if needed
set family id (only needed for bootstrap)
B number of boostrap samples (only needed for bootstrap)
logrank if logrank test is desired
subset logical condition to subset data
trace Show iterations for bootstrap

Value

object of classes "kin.cohort" and "wacholder".

cumrisk matrix of dimension (number of knots x 3) with cumulative risk festimates or noncarriers, carriers and the cumulative risk ratio
knots vector of knots
km object class survfit (package survival)
logrank p-value of the logrank test
events matrix with number of events and person years per each knot
call copy of call


if bootstrap confidence intervals are requested (B>1) then the returned object is of classes "kin.cohort.boot" and "wacholder" with previous items packed in value estimate and each bootstrap sample packed in matrices.

Note

This function is best called by kin.cohort than directly

References

Wacholder S, Hartge P, Struewing JP, Pee D, McAdams M, Lawrence B, Tucker MA. The kin-cohort study for estimating penetrance. American Journal of Epidemiology. 1998; 148: 623-9.

See Also

kin.cohort, print.kin.cohort, plot.kin.cohort

Examples

data(kin.data)
attach(kin.data)
res.km<- kc.moments(age, cancer, gen1, rel, knots=c(30,40,50,60,70,80), f=0.02)
res.km

[Package kin.cohort version 0.6 Index]