|Description||TP53 mutation carrier estimation for families with Li-Fraumeni syndrome.|
|Citations||Peng G, Bojadzieva J, Ballinger ML, Thomas DM, Strong LC, Wang W✉. Estimating TP53 Mutation Carrier Probability in Families with Li-Fraumeni Syndrome Using LFSPRO. Cancer Epidemiology, Biomarker and Prevention Jan 2017. DOI: 10.1158/1055-9965.EPI-16-0695.|
|News||A new version is now available.|
|Help and Support|
Germline TP53 mutation is a main cause for the Li-Fraumeni Syndrome. This package is designed to estimate the probability that the counselee carries a germ line TP53 deleterious mutation based on his/her family cancer history. We also provide functions for decision based on the commonly used clinical criteria: the classic  and Chompret criteria  in the package.
LFSPRO is now available from inside the BayesMendel R package. You can download from here: BayesMendel version 2.1-2
Source File: LFSPRO_1.0.5.tar.gz
Mac OS: LFSPRO_1.0.5.tgz
Windows 10: LFSPRO_1.0.5.zip R packages for old versions of Windows are available upon request.
Warning: An error may occur when installing the package in Mac OS X Yosemite. It may caused by the incompatibility between R and the Yosemite system. Please let us know if you encounter any such problems.
After downloading the R package, for Unix alike system type the following command in the command line to install the package:
R CMD INSTALL LFSPRO_1.0.5.tar.gz
R CMD INSTALL LFSPRO_1.0.5.tgz
R CMD INSTALL LFSPRO_1.0.5.zip
Check here for details of R package installation.
The details about how to install R and LFSPRO package, please check the #Documentation.
LFSPRO requires two data sets as input. One data set stores the pedigree information and the other stores the cancer information.
The structure of the pedigree information data is described below:
Example: For the pedigree shown below, it can be stored in the pedigree information data file on its right:
The cancer information data stores the following information about the cancer:
The following code briefly illustrates how to used the package. Check the manual for details.
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) # LFS classic criteria LFSClassic(fam.data, cancer.data, counselee.id) # Chompret criteria LFSChompret(fam.data, cancer.data, counselee.id) allef.g <- list(c(0.9999,0.0001)) mRate.g <- 5e-4 # LFSPRO LFSPRO(fam.data, cancer.data, LFSpenet.2010, counselee.id, allef.g, 1,mRate.g)
The TP53 mutation carrier probability for each counselee. It is a data frame with 3 variables: fam.id (family id), id (individual id) and pp(posterior probability that the counselee is a TP53 mutation carrier).
Here you can download the standard R documentation for LFSPRO.