calLK.cs: Calculate the likelihood Pr(D|G) for cancer specific.

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

Calculate the likelihood Pr(D|G) for cancer specific.

Description

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

Usage

  calLK.cs(ind.data, penetrance.all, 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.
penetrance.all	The penetrance of three genotype (wild type, one copy and two copies of TP53 mutated alleles) for male and female in the population. See lfspenet.cs 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., Yuan, Y., Strong, L. C., Bojadzieva, J., and Wang, W. (2018). Bayesian Semiparametric Estimation of Cancer-Specific Age-at-Onset Penetrance With Application to Li-Fraumeni Syndrome. Journal of the American Statistical Association, 1–12. https://doi.org/10.1080/01621459.2018.1482749

See Also

lkNoneAffect.cs, lfsproC.cs, peelingRC

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.cs(data.obj2[[1]], lfspenet.cs)

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