kc.moments: Kin-cohort estimation of penetrance by the method of moments

In kin.cohort: Analysis of Kin-Cohort Studies

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

## Not run: 
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

## End(Not run)

kin.cohort documentation built on May 1, 2019, 9:15 p.m.