Man pages for RVS
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 |
