Computes estimates of the probability of related individuals sharing a rare variant

ancestorDistance | distance between a descendant and an ancestor |

areMating | determine if two subjects have a child together |

checkArgs | check arguments provided to RVsharing for validty |

ComputeKinshipPropCoef-methods | ratio of excess kinship among descendants over mean kinship... |

computePFU | computation of P[FjU] using equation 21 of Bureau et al. |

computePhiVec | expected kinship coefficient for different number of alleles |

convertMatrix | convert snpMatrix to a list of vectors of sharing |

createNetwork | create bayesian network from processed pedigree |

denomProb | denominator of sharing probability |

enrichmentPValue | enrichment p-value across multiple families and variants |

enrichmentPValue_R_Backend | R backend for enrichmentPValue calculation |

exactSharingProb | exact sharing probability calculation |

ex.ped.mat | matrix of pedigree information and genotype data from famVCF... |

extract_carriers | extract carriers of minor allele |

fam15157.vcf | VCF objects containing genotype data for two families:... |

fam28003.vcf | VCF objects containing genotype data for two families:... |

founderOccurence | determine if subjects are descended from founders |

GeneDrop | deprecated function |

get.psubset | deprecated function |

inferNumAlleles | most likely number of distinct alleles among founders |

inferTheta | solve the parameter theta for polynomial approximation of the... |

isDescendant | determine if one subject is a descendant of another |

marginalProb | calculates the marginal probability of a set of nodes |

monteCarloSharingProb | calculates sharing probability by simulating pedigree... |

multipleFamilyPValue | probability of sharing of rare variants in a subset of... |

multipleFamilyPValue_R_Backend | R backend for multipleFamilyPValue calculation |

multipleVariantPValue | generalization of multipleFamilyPValue to multiple variants |

multipleVariantPValue_R_Backend | R backend for multipleVariantPValue calculation |

numerProb | numerator of sharing probability |

oldArgs | check for arguments in v1.7 format |

oneFounderSharingProb | calculate sharing probability in basic case |

oneFounderSharingProbSplitting | calculate sharing probability in basic case |

ped2trio | deprecated function |

processPedigree-methods | extract useful information from a pedigree |

relatedFoundersCorrection | make the neccesary correction for when founders have a... |

runMonteCarlo | run the monte carlo simulation |

RVgene | Probability of sharing of rare variants in a family sample... |

RVS | RVS |

RVsharing-methods | probability of sharing a rare variant among relatives |

samplePedigrees | list of 8 sample pedigree objects |

simulatePedigree | simulates pedigree given founder states |

snpMat | SnpMatrix with genotype information from famVCF for fam15157 |

SnpMatrixToCount | convert a list of SnpMatrices to a single matrix in a... |

twoFounderSharingProb | sharing probability when founder pair introduces variant |

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