lfspro {LFSPRO} | R Documentation |
We use Mendelian risk prediction model to estimate the probability for the counselee as a TP53 mutation carrier on the basis of his/her family cancer history.
lfspro(fam.data, cancer.data, penetrance.all, counselee.id, allef, nloci, mRate)
fam.data |
Family information data. See fam.data for details. |
cancer.data |
Cancer information data. See cancer.data for details. |
penetrance.all |
Penetrance data. See LFSpenet.2010 for details. |
counselee.id |
Data frame including two variables: fam.id (family id of counselees) and id (individual id of counselees). |
allef |
List. Allele frequency for each locus/gene. If there is only one gene and two alleles in the gene (allele frequency is 0.1 and 0.9), allef = list(c(0.1,0.9)), If there are two genes,two alleles (allele frequency is 0.1 and 0.9) for gene 1 and three alleles (allele frequncy is 0.2, 0.2 and 0.6) for gene 2, allef = list(c(0.1,0.9),c(0.2,0.2,0.6)). We suggeste to use list(c(1-maf,maf)). maf = 0.0001. |
nloci |
Number of loci/genes in the model. It is set to be 1 here. |
mRate |
Mutation rate. We suggest to use 5e-4. |
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).
Gang Peng, Wenyi Wang
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.
LFSClassic
, LFSChompret
, lfsproC
allef.g <- list(c(0.9997,0.0003)) mRate.g <- 6e-05 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) lfspro(fam.data, cancer.data, LFSpenet.2010, counselee.id, allef.g, 1,mRate.g)