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| LFSPRO-package | TP53 mutation carrier estimation and cancer risk predictions |
| calLK | Calculate the likelihood Pr(D|G). |
| calLK.cs | Calculate the likelihood Pr(D|G) for cancer specific. |
| calLK.mpc | Calculate the likelihood Pr(D|G) of multiple primary cancers. |
| cancer.data | Built-in Cancer Information Data example |
| cancer.type.all | Predefined cancer types in LFSPRO. |
| combined.risk.mpc | Calculate the future cancer risk using the MPC model |
| combinedata | Combine the family information data and cancer information data |
| convert.data | Convert the combined family information data and cancer information data into separate data objects. |
| fam.cancer.data | Data object with Family and Cancer Information Example |
| fam.data | Built-in Family Information Data Example |
| firstDegreeRelative | First degree relatives |
| invasive.cut | Cutoff for malignant cancer |
| lfs.cut | Cutoff for Li-Fraumeni Syndrome spectrum cancer |
| lfsChompret2009 | The Chompret criteria for Li-Fraumeni syndrome |
| lfsChompret2015 | The Chompret criteria for Li-Fraumeni syndrome |
| lfsClassic | The Classic criteria for Li-Fraumeni syndrome |
| lfspenet.2010 | Penetrance for TP53 mutations |
| lfspenet.cs.death | Penetrance table for cancer-specific mutation with four competing risks (breast cancer, sarcoma, other cancers and death). |
| lfspenet.cs.nodeath | Penetrance table for cancer-specific mutation with three competing risks (breast cancer, sarcoma and other cancers). Default penetrance table in predicting cancer-specific risks. |
| lfspro.cancer.type | Predefined cancer types and the corresponding number in lfspro |
| lfspro.mode | Estimate TP53 mutation probability and predict cancer risk for families with Li-Fraumeni Syndrome with mode choice |
| lfsproC | Calculate the posterior probability of p53 mutations on the basis of family history |
| lfsproC.cs | Calculate the posterior probability of p53 mutations for cancer-specific risk prediction model on the basis of family history |
| lfsproC.mpc | Calculate the posterior probability of p53 mutations for multiple primary cancer on the basis of family history |
| lkNoneAffect | Likelihood for un-affected individuals |
| lkNoneAffect.cs | Likelihood for un-affected individuals for cancer-specific model |
| parameter.mpc | Estimated parameter for semiparametric recurrent event model of multiple primary cancers |
| peelingRC | Peeling interface in R. |
| reformatForClassicChompret | Reformat input data of LFSPRO for evaluation using the Classic or the Chompret criteria |
| risk.cs | Predict the cancer-specific risk |
| risk.mpc | Predict the risks of developing multiple primary cancers |
| secondDegreeRelative | Second degree relative |