LFSPRO-package {LFSPRO}R Documentation

TP53 mutation carrier estimation

Description

TP53 mutation is a main cause of Li-Fraumeni syndrome. This package is designed to estimate the probability that the counselee is a TP53 mutation carrier on the basis of his/her family cancer history. We also included LFS classic and Chompret criteria in the package.

Details

Package: LFSPRO
Type: Package
Version: 1.0.5
Date: 2016-12-14
License: GPL-3

Note

New features in 1.0.5: (1) add function LFSChompret2015, (2) update the the default MAF and de novo mutation rate.

Author(s)

Gang Peng, Wenyi Wang

Maintainer: Gang Peng <michael.gang.peng@gmail.com>

References

Peng, G., Bojadzieva, J., Ballinger, M., Thomas, D., Strong, L. and Wang, W. Estimating TP53 Mutation Carrier Probability in Families with Li-Fraumeni Syndrome Using LFSpro. Submitted.

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.

See Also

lfspro, LFSClassic, LFSChompret

Examples

options(stringsAsFactors = FALSE)
fam.id <- c("fam1","fam2","fam2","fam2","fam2")
id <- c(0,0,2,100,200)
counselee.id <- data.frame(fam.id, id)
LFSClassic(fam.data, cancer.data, counselee.id)
LFSChompret(fam.data, cancer.data, counselee.id)

allef.g <- list(c(0.9997,0.0003))
mRate.g <- 6e-05

lfspro(fam.data, cancer.data, LFSpenet.2010, counselee.id, allef.g, 1,mRate.g)

[Package LFSPRO version 1.0.5 Index]