LFSPRO-package {LFSPRO} | R Documentation |
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.
Package: | LFSPRO |
Type: | Package |
Version: | 1.0.5 |
Date: | 2016-12-14 |
License: | GPL-3 |
New features in 1.0.5: (1) add function LFSChompret2015, (2) update the the default MAF and de novo mutation rate.
Gang Peng, Wenyi Wang
Maintainer: Gang Peng <michael.gang.peng@gmail.com>
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.
lfspro
, LFSClassic
, LFSChompret
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)