risk.cs: Predict the cancer-specific risk

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

Predict the cancer-specific risk

Description

Predict the future risks of having breast cancer, sarcoma and other cancers, who never had cancers.

Usage

  risk.cs(fam.cancer.data, penetrance.all, counselee.id, posterior)

Arguments

fam.cancer.data	Data frame storing family and cancer information. See fam.cancer.data for details.
penetrance.all	List. Two lists indicate the cancer-specific penetrances of male and female (fMX: male, fFX: female), respectively. For each list, it contains 4 of 110x3 penetrance matrices, row: from age 1 to age 110, column: three kinds of genotype: P530 (wild type, neither of allele mutated), P531 (one allele mutated in P53) and P532 (two allele mutated in P53). Each matrix represents one penetrance matrix of breast cancer, sarcoma, other cancers, and death, respectively. See lfspenet.cs 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 the samples.
posterior	Posterior probability of carrying TP53 mutation

Value

List. Each matrix of the list indicates the risks of counselees in 5, 10, 15, 20 years of having breast cancer, sarcoma and other cancers, respectively.

Author(s)

Nam Nguyen

Examples

nloci <- 1 
allef <- list(c(1 - 1.0e-4, 1.0e-4))
counselee.id <- data.frame(fam.data[1:5,1:2]) 
mRate <- 1.0e-6
cancer.data <- data.frame(fam.id = c("fam1", "fam1", "fam1"),
                          id = c(0,2,4),
                          cancer.type = c(2,4,1),
                          diag.age = c(12,50,14))
fam.cancer.data <- combinedata(fam.data, cancer.data) 
cid <- c(0,5,10)
pp <- lfsproC.cs(fam.cancer.data[[1]], lfspenet.cs, 
                 cid, allef, nloci, mRate)
risk.cs(fam.cancer.data[[1]], lfspenet.cs, cid, pp)

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