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

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Documentation for package ‘RVS’ version 1.29.0

• DESCRIPTION file.
• User guides, package vignettes and other documentation.
• Package NEWS.

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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
convertMatrix	convert snpMatrix to a list of vectors of sharing
enrichmentPValue	enrichment p-value across multiple families and variants
enrichmentPValue_R_Backend	R backend for enrichmentPValue calculation
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
multipleFamilyPValue_R_Backend	R backend for multipleFamilyPValue calculation
multipleVariantPValue	generalization of multipleFamilyPValue to multiple variants
multipleVariantPValue_R_Backend	R backend for multipleVariantPValue calculation
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