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


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Documentation for package ‘RVS’ version 1.0.0

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RVS-package RVS
ComputeKinshipPropCeof ratio of excess kinship among descendants over mean kinship among founders
ComputeKinshipPropCoef ratio of excess kinship among descendants over mean kinship among founders
ComputeKinshipPropCoef-method ratio of excess kinship among descendants over mean kinship among founders
ex.ped.mat matrix of pedigree information and genotype data from famVCF stored in the LINKAGE format
fam15157.vcf VCF objects containing genotype data for two families: fam15157 and fam28003 (corresponding to the secondCousinTriple and firstAndSecondCousinsTriple families in samplePedigrees)
fam28003.vcf VCF objects containing genotype data for two families: fam15157 and fam28003 (corresponding to the secondCousinTriple and firstAndSecondCousinsTriple families in samplePedigrees)
GeneDrop deprecated function
GeneDropSim.allsubsets.fn deprecated function
GeneDropSim.fn deprecated function
GeneDropSimExcessSharing.fn deprecated function
get.psubset deprecated function
multipleFamilyPValue probability of sharing of rare variants in a subset of families
ped2trio deprecated function
processPedigree extract useful information from a pedigree
processPedigree-method extract useful information from a pedigree
RVgene Probability of sharing of rare variants in a family sample within a gene
RVS RVS
RVsharing probability of sharing a rare variant among relatives
RVsharing-method probability of sharing a rare variant among relatives
samplePedigrees list of 8 sample pedigree objects
snpMat SnpMatrix with genotype information from famVCF for fam15157
SnpMatrixToCount convert a list of SnpMatrices to a single matrix in a similiar format as LINKAGE except with minor allele counts