lfsproC: Calculate the posterior probability of p53 mutations on the...

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

Calculate the posterior probability of p53 mutations on the basis of family history

Description

lfsproC is used to calculate posterior probability of carrying p53 mutation on the baisis of counselees' family cancer history.

Usage

lfsproC(fam.cancer.data, penetrance.all, counselee.id, allef, nloci, mRate)

Arguments

fam.cancer.data	Combined family and cancer information data for ONE FAMILY ONLY. See fam.cancer.data for details.
penetrance.all	Penetrance data. See lfspenet.2010 for details.
counselee.id	Individual id for the counselee. If you want to estimate multiple samples at the same time, just set counselee.id as a vector of IDs for all.
allef	List. Allele frequency for each locus/gene. If there is only one gene and two alleles in the gene (allele frequency is 0.1 and 0.9), allef = list(c(0.1,0.9)), If there are two genes,two alleles (allele frequency is 0.1 and 0.9) for gene 1 and three alleles (allele frequncy is 0.2, 0.2 and 0.6) for gene 2, allef = list(c(0.1,0.9),c(0.2,0.2,0.6)). We set it as allef=list(c(0.9994,0.0006)) by default.
nloci	Number of loci/genes in the model. It's set to be 1 here.
mRate	Mutation rate. We set it as 0.00012 by default.

Value

A data frame of posterior probabilities of having wild type, one allele mutated and two allels mutated in TP53 for each counselee.

Author(s)

Gang Peng, Wenyi Wang

References

Peng, G., Bojadzieva, J., Ballinger, M. L., Li, J., Blackford, A. L., Mai, P. L., Savage, S. A., Thomas, D. M., Strong, L. C., … Wang, W. (2017). Estimating TP53 Mutation Carrier Probability in Families with Li-Fraumeni Syndrome Using LFSPRO. Cancer Epidemiology, Biomarker and Prevention, 26(6), 837-844. DOI: 10.1158/1055-9965.EPI-16-0695

Chen, S., Wang, W., Broman, K. and Parmigiani, G. (2004) BayesMendel: An R Environment for Mendelian Risk Prediction. Statistical Application in Genetics and Molecular Biology, 3(1): Article 21. DOI: 10.2202/1544-6115.1063

See Also

lfsClassic, lfsChompret2009, lfsChompret2015, lfspro, peelingRC

Examples

# convert cancer type to specific number and check the cancer type
cancer.data$cancer.type <- c(2,4,3,7,2,2,6,50,50,2,4,50,50,4,50) #cancer types
allef <- allef.g <- list(c(0.9997,0.0003))
mRate.g <- 6e-05
fam.cancer.data <- combinedata(fam.data, cancer.data)
lfsproC(fam.cancer.data[[1]], lfspenet.2010, 0, allef.g, 1,mRate.g)

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