|Description||Estimate the probability of deleterious germline mutations to be de novo using family history data.|
|News||Version 0.1.1 is now available|
|Citation||A pedigree-based prediction model identifies carriers of deleterious de novo mutations in families with Li-Fraumeni syndrome. Gao F, et al.|
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|Discussion||Issues On GitHub|
Famdenovo is an algorithm that calculates the probability of de novo status in deleterious germline mutations using family history data. We demonstrate the utility of Famdenovo using deleterious TP53 mutations, which is a major cause for the Li-Fraumeni Syndrome , as de novo TP53 mutations account for 7-20% of the LFS patients.1,2
Source File: Famdenovo_0.1.1.tar.gz . The source file is compatible with windows, linux and mac os.
For details about how to install and use Famdenovo, please check the Manual .
After downloading the R package, type the following command in the command line:
R CMD INSTALL Famdenovo_0.1.1.tar.gz
Or type the following command in R Console to install the package:
install.packages("Famdenovo_0.1.1.tar.gz", repos = NULL)
You can also install from GitHub:
Check here for details of R package installation.
Famdenovo requires the following information as input: family, cancer, person.id, mutation, and gene.
The input should be a data frame. The family data should include the following columns with the corresponding column names:
Example: For the pedigree shown below, pedigree information is stored as shown in the data file on its right:
The input should be a data frame. The cancer data should include the following columns with the corresponding column names:
The input should be a data frame. The mutation data should include the following columns with the corresponding column names:
The input should be either character string(s) or numerical value(s) of the person(s) you want to analyze.
The input should be character string(s). The default value is “TP53”. We have recently extended the Famdenovo function to BRCA1/2 as described above.
Famdenovo(family, cancer, mutation, person.id, gene = "TP53")
The following example briefly illustrates how to use the package.
library(Famdenovo) # Test case 1 data(TP53.test1.family) data(TP53.test1.cancer) data(TP53.test1.mutation) person.id <- c(2201, 2203, 3201, 3202, 4203) output1 <- Famdenovo(TP53.test1.family, TP53.test1.cancer, person.id, TP53.test1.mutation) output1 # Test case 2 data(TP53.test2.family) data(TP53.test2.cancer) person.id <- c(1, 11, 12, 13) output2 <- Famdenovo(TP53.test2.family, TP53.test2.cancer, person.id) output2
Currently we apply Famdenovo to the cancer gene TP53. The output of Famdenovo is the probability of a deleterious TP53 mutation being de novo.
# Test case 1  "The following ids are not carriers: 3202, 4203" id prob.denovo 1 2201 0.0001205471 2 2203 0.0001105599 3 3201 0.0126455556 # Test case 2  "Warning: Famdenovo output is only applicatble to mutation carriers" id prob.denovo 1 1 0.999994634 2 11 0.003633958 3 12 0.003774075 4 13 0.100231438
The Shiny App for Famdenovo is also available. It is an interactive web app using the same inputs as the R software does. The output contains a pedigree structure of the family, the cancer information, and the de novo probability of mutation carriers calculated by Famdenovo.