Package: RVS 1.29.0
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:
RVS_1.29.0.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')) |
- 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-1.29.0(bioc 3.21)RVS-1.28.0(bioc 3.20)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
immunooncologygeneticsgenomewideassociationvariantdetectionexomeseqwholegenome
Last updated 25 days agofrom:b6690b7afe. Checks:OK: 1 WARNING: 6. Indexed: yes.
Target | Result | Date |
---|---|---|
Doc / Vignettes | OK | Oct 31 2024 |
R-4.5-win | WARNING | Oct 31 2024 |
R-4.5-linux | WARNING | Oct 31 2024 |
R-4.4-win | WARNING | Oct 31 2024 |
R-4.4-mac | WARNING | Oct 31 2024 |
R-4.3-win | WARNING | Oct 31 2024 |
R-4.3-mac | WARNING | Oct 31 2024 |
Exports:ComputeKinshipPropCoefenrichmentPValueGeneDropGeneDropSim.allsubsets.fnGeneDropSim.fnGeneDropSimExcessSharing.fnget.psubsetmultipleFamilyPValuemultipleVariantPValueped2trioprocessPedigreeRVgeneRVsharingSnpMatrixToCount
Dependencies:backportsBHBiocGenericsbootstrapbroomclicodetoolscpp11doParalleldplyrevaluatefansiforeachgenericsGENLIBgluegRaingRbasehighrigraphiteratorskinship2knitrlatticelifecyclemagrittrMatrixpillarpkgconfigpurrrquadprogR.methodsS3R.ooR.utilsR6RcppRcppArmadilloRcppEigenrlangsnpStatsstringistringrsurvivaltibbletidyrtidyselectutf8vctrswithrxfunyamlzlibbioc