combined.risk.mpc: Calculate the future cancer risk using the MPC model

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

Calculate the future cancer risk using the MPC model

Description

Calculate the future cancer risk of each individual who is either healthy or has only been diagnosed with one primary cancer using our MPC model (this model cannot predict the cancer risks for patients who have had multiple primary cancer).

Usage

  combined.risk.mpc(posterior, risk, counselee.id)

Arguments

posterior	Genotype likelihood, n*3 matrix.
risk	Matrix, future cancer risks for each genotype, wild-type and mutated, in 5 years, 10 years and 15 years.
counselee.id	Data frame including two variables: fam.id (family ids of counselees) and id (individual ids of counselees).

Value

Matrix, family ID, personal ID and the future cancer risks in 5, 10 and 15 years.

Author(s)

Jingxiao Chen

Examples

counselee.id <- data.frame(fam.id = "fam1", cid=1)
pp <- matrix(c(0.365762982, 0.634046770, 1.902481e-04),nrow=1, ncol=3)
risk <- matrix(c("fam1",1,35,0.008601,0.103538,0.020350,0.220971,0.035787,0.3410216),
               nrow=1, ncol=9)
colnames(risk) <- c("fam.id", "ID", "age","5 years(wildtype)", "5 years(mutation)", 
                    "10 years(wildtype)", "10 years(mutation)", "15 years(wildtype)", 
                    "15 years(mutation)")
combined.risk.mpc(pp, risk, counselee.id)

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