Package: RVS 1.35.0

Alexandre Bureau

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

Rare Variant Sharing (RVS) implements tests of association and linkage between rare genetic variant genotypes and a dichotomous phenotype, e.g. a disease status, in family samples. The tests are based on probabilities of rare variant sharing by relatives under the null hypothesis of absence of linkage and association between the rare variants and the phenotype and apply to single variants or multiple variants in a region (e.g. gene-based test).

Authors:Alexandre Bureau, Ingo Ruczinski, Samuel Younkin, Thomas Sherman

RVS_1.35.0.tar.gz
RVS_1.35.0.zip(r-4.7)RVS_1.35.0.zip(r-4.6)RVS_1.35.0.zip(r-4.5)
RVS_1.35.0.tgz(r-4.6-any)RVS_1.35.0.tgz(r-4.5-any)
RVS_1.35.0.tar.gz(r-4.7-any)RVS_1.35.0.tar.gz(r-4.6-any)
RVS_1.35.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html
card.svg |card.png
RVS/json (API)
NEWS

# Install 'RVS' in R:
install.packages('RVS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))
Datasets:
  • 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
  • fam28003.vcf - VCF objects containing genotype data for two families: fam15157 and fam28003
  • samplePedigrees - List of 8 sample pedigree objects
  • snpMat - SnpMatrix with genotype information from famVCF for fam15157

On BioConductor:RVS-1.35.0(bioc 3.24)RVS-1.34.0(bioc 3.23)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

immunooncologygeneticsgenomewideassociationvariantdetectionexomeseqwholegenome

4.98 score 16 scripts 350 downloads 6 mentions 14 exports 50 dependencies

Last updated from:91844438b1. Checks:1 ERROR, 7 WARNING, 2 OK. Indexed: yes.

TargetResultTimeFilesSyslog
bioc-checksERROR178
linux-devel-x86_64WARNING321
source / vignettesOK345
linux-release-x86_64WARNING368
macos-release-arm64WARNING179
macos-oldrel-arm64WARNING245
windows-develWARNING241
windows-releaseWARNING241
windows-oldrelWARNING201
wasm-releaseOK159

Exports:ComputeKinshipPropCoefenrichmentPValueGeneDropGeneDropSim.allsubsets.fnGeneDropSim.fnGeneDropSimExcessSharing.fnget.psubsetmultipleFamilyPValuemultipleVariantPValueped2trioprocessPedigreeRVgeneRVsharingSnpMatrixToCount

Dependencies:backportsBHBiocGenericsbootstrapbroomclicodetoolscpp11doParalleldplyrevaluateforeachgenericsGENLIBgluegRaingRbasehighrigraphiteratorskinship2knitrlatticelifecyclemagrittrMatrixpillarpkgconfigpurrrquadprogR.methodsS3R.ooR.utilsR6RcppRcppArmadilloRcppEigenrlangsnpStatsstringistringrsurvivaltibbletidyrtidyselectutf8vctrswithrxfunyaml

The RVS (Rare Variant Sharing) Package

Rendered fromRVS.Rmdusingknitr::rmarkdownon May 30 2026.

Last update: 2019-04-01
Started: 2017-07-12

Readme and manuals

Help Manual

Help pageTopics
ratio of excess kinship among descendants over mean kinship among foundersComputeKinshipPropCeof ComputeKinshipPropCoef ComputeKinshipPropCoef,pedigree-method
convert snpMatrix to a list of vectors of sharingconvertMatrix
enrichment p-value across multiple families and variantsenrichmentPValue
R backend for enrichmentPValue calculationenrichmentPValue_R_Backend
matrix of pedigree information and genotype data from famVCF stored in the LINKAGE formatex.ped.mat
VCF objects containing genotype data for two families: fam15157 and fam28003 (corresponding to the secondCousinTriple and firstAndSecondCousinsTriple families in samplePedigrees)fam15157.vcf
VCF objects containing genotype data for two families: fam15157 and fam28003 (corresponding to the secondCousinTriple and firstAndSecondCousinsTriple families in samplePedigrees)fam28003.vcf
deprecated functionGeneDrop GeneDropSim.allsubsets.fn GeneDropSim.fn GeneDropSimExcessSharing.fn
deprecated functionget.psubset
probability of sharing of rare variants in a subset of familiesmultipleFamilyPValue
R backend for multipleFamilyPValue calculationmultipleFamilyPValue_R_Backend
generalization of multipleFamilyPValue to multiple variantsmultipleVariantPValue
R backend for multipleVariantPValue calculationmultipleVariantPValue_R_Backend
deprecated functionped2trio
extract useful information from a pedigreeprocessPedigree processPedigree,pedigree-method
Probability of sharing of rare variants in a family sample within a geneRVgene
RVSRVS
probability of sharing a rare variant among relativesRVsharing RVsharing,list-method RVsharing,pedigree-method
list of 8 sample pedigree objectssamplePedigrees
SnpMatrix with genotype information from famVCF for fam15157snpMat
convert a list of SnpMatrices to a single matrix in a similiar format as LINKAGE except with minor allele countsSnpMatrixToCount