Package: RVS 1.27.0

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_1.27.0.tar.gz
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RVS.pdf |RVS.html✨
RVS/json (API)
NEWS

# Install 'RVS' in R:
install.packages('RVS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

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-1.27.0(bioc 3.20)RVS-1.26.0(bioc 3.19)

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

bioconductor-package

14 exports 0.91 score 52 dependencies 6 mentions

Last updated 2 months agofrom:3a75dc636c

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

Dependencies:backportsBHBiocGenericsbootstrapbroomclicodetoolscpp11doParalleldplyrevaluatefansiforeachgenericsGENLIBgluegRaingRbasehighrigraphiteratorskinship2knitrlatticelifecyclemagrittrMatrixpillarpkgconfigpurrrquadprogR.methodsS3R.ooR.utilsR6RcppRcppArmadilloRcppEigenrlangsnpStatsstringistringrsurvivaltibbletidyrtidyselectutf8vctrswithrxfunyamlzlibbioc

The RVS (Rare Variant Sharing) Package

Alexandre Bureau, Ingo Ruczinski, Samuel Younkin, Thomas Sherman

Rendered fromRVS.Rmdusingknitr::rmarkdownon Jun 30 2024.

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