calLK.mpc: Calculate the likelihood Pr(D|G) of multiple primary cancers.

In wwylab/LFSPRO: TP53 germline mutation carrier estimation and cancer risk predictions

Calculate the likelihood Pr(D|G) of multiple primary cancers.

Description

Calculate the likelihood (Pr(D|G), the probability of disease status D given the genotype G for each individual in the family.

Usage

  calLK.mpc(ind.data, parameter, mut.info)

Arguments

ind.data	A comprehensive dataset that describes each individual in details, including age, gender (1 for male, 2 for female), mutation status (0 for wildtype, 1 for mutation, NA if unknown), vital status (A if alive, D if dead), and cancer history (cancer type and age at diagnosis). Both data1 and data2 can be generated from family and cancer datasets using combinedata and convert.data. See the example below.
parameter	Parameter estimates for semiparametric recurrent event model of multiple primary cancers. See parameter.mpc for details.
mut.info	Set to TRUE (default) if you want to use known genetic testing results of family members in the calculation of mutation probabilities. Set to FALSE otherwise.

Value

Return a n*3 matrix. The likelihood of observing the cancer outcome given genotype for each individual in the family. n denotes the total number of individuals in the family.

Author(s)

Seung Jun Shin, Nam Nguyen

References

Shin, S. J., Ning, J., Bojadzieva, J., Strong, L. C., and Wang, W. (2018). Bayesian estimation of a semiparametric recurrent event model with applications to the penetrance estimation of multiple primary cancers in Li-Fraumeni syndrome. Biostatistics, 00, 1–16. https://doi.org/10.1093/biostatistics/kxy066

See Also

lfsproC.mpc

Examples

fam.cancer.data <- combinedata(fam.data, cancer.data)
data.obj <- convert.data(fam.cancer.data)
data.obj1 <- data.obj[[1]]
data.obj2 <- data.obj[[2]]
calLK.mpc(data.obj2[[1]], parameter.mpc)

wwylab/LFSPRO documentation built on Feb. 1, 2023, 1:05 a.m.