Package: Ravages 1.1.3

Ravages: Rare Variant Analysis and Genetic Simulations

Rare variant association tests: burden tests (Bocher et al. 2019 <doi:10.1002/gepi.22210>) and the Sequence Kernel Association Test (Bocher et al. 2021 <doi:10.1038/s41431-020-00792-8>) in the whole genome; and genetic simulations.

Authors:Ozvan Bocher and Hervé Perdry

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NEWS

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

Peer review:

Uses libs:
  • c++– GNU Standard C++ Library v3
Datasets:

On CRAN:

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

34 exports 0.00 score 61 dependencies 2 scripts 319 downloads

Last updated 1 years agofrom:e72329ca75. Checks:OK: 1 WARNING: 8. Indexed: yes.

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Doc / VignettesOKSep 03 2024
R-4.5-win-x86_64WARNINGSep 03 2024
R-4.5-linux-x86_64WARNINGSep 03 2024
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R-4.3-win-x86_64WARNINGSep 03 2024
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Exports:adjustedCADD.annotationadjustedCADD.annotation.indelsadjustedCADD.annotation.SNVsbed.matrix.split.genomic.regionburdenburden.continuousburden.continuous.subscoresburden.mlogitburden.mlogit.subscoresburden.subscoresburden.weighted.matrixCASTfilter.adjustedCADDfilter.rare.variantsgenotypic.freqGRR.matrixJaccardmultinomial.asso.freqNullObject.parametersRAVA.FIRSTrbm.GRRrbm.GRR.powerrbm.haplos.freqsrbm.haplos.powerrbm.haplos.thresholdsset.CADDregionsset.genomic.regionset.genomic.region.subregionSKATSKAT.bootstrapSKAT.continuousSKAT.permutationsSKAT.theoreticalWSS

Dependencies:bedrBHbriocallrclicrayoncurldata.tabledescdfidxdiffobjdigestdplyrevaluatefansiformatRFormulafsfutile.loggerfutile.optionsgastongenericsgluejsonlitelambda.rlatticelifecyclelmtestmagrittrMASSmlogitpillarpkgbuildpkgconfigpkgloadpraiseprocessxpsR.methodsS3R.ooR.utilsR6rbibutilsRcppRcppEigenRcppParallelRdpackrematch2rlangrprojrootstatmodtestthattibbletidyselectutf8vctrsVennDiagramwaldowithryamlzoo

Package Ravages (RAre Variant Analysis and GEnetic Simulation), Simulations

Herve Perdry and Ozvan Bocher

Rendered fromRavages_Simulations_vignette.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2022-06-01
Started: 2020-11-11

Package Ravages (RAre Variant Analysis and GEnetic Simulation)

Herve Perdry and Ozvan Bocher

Rendered fromRavages_vignette.Rmdusingknitr::rmarkdownon Sep 03 2024.

Last update: 2022-06-01
Started: 2020-11-11

Readme and manuals

Help Manual

Help pageTopics
SNVs and Indels annotation with adjusted CADD scoresadjustedCADD.annotation
Indels annotation with adjusted CADD scoresadjustedCADD.annotation.indels
SNVs annotation with adjusted CADD scoresadjustedCADD.annotation.SNVs
Bed matrix for variants associated to multiple genomic regionsbed.matrix.split.genomic.region
Linear, logistic or multinomial regression on a genetic scoreburden
Linear regression on a genetic scoreburden.continuous
Linear regression on a multiple genetic scores within a genomic regionburden.continuous.subscores
Logistic or multinomial regression on a genetic scoreburden.mlogit
Logistic or multinomial regression on a multiple genetic scores within a genomic regionburden.mlogit.subscores
Linear, logistic or multinomial regression on a multiple genetic scores within a genomic regionburden.subscores
Score matrix for burden testsburden.weighted.matrix
Cohort Allelic Sum TestCAST
Variant filtering based on frequency and median adjusted CADD by CADD regionsfilter.adjustedCADD
Rare variants filteringfilter.rare.variants
Genes positionsgenes.b37 genes.b38 genes.positions
Genotypic frequencies calculation for data simulationsgenotypic.freq
GnomADgenes datasetGnomADgenes
GRR matrix for genetic data simulationGRR.matrix
Jaccard indexJaccard
Kryukov data setKryukov
LCT haplotypes data setLCT.hap LCT.haplotypes LCT.sample LCT.snps
LCT genotypes matrixLCT.matrix LCT.matrix.bed LCT.matrix.fam LCT.matrix.pop1000G
Single variant association test with categorical phenotypemultinomial.asso.freq
Null Model for SKAT and burden testsNullObject.parameters
RAVA-FIRST: RAre Variant Association using Functionally-InfoRmed STepsRAVA.FIRST
Simulation of genetic data using GRR valuesrbm.GRR
Power of RVAT based on simulations and theoretical calculations (CAST) with GRRrbm.GRR.power
Simulation of genetic data based on haplotypic frequenciesrbm.haplos.freqs
Power of RVAT based on simulations with haplotypesrbm.haplos.power
Simulation of genetic data based on haplotypes and a libaility modelrbm.haplos.thresholds
Variants annotation based on 'CADD regions' and genomic categoriesset.CADDregions
Variants annotation based on gene positionsset.genomic.region
Variants annotation based on regions and subregions positionsset.genomic.region.subregion
SKAT testSKAT
Multi group SKAT test using bootstrap samplingSKAT.bootstrap
Multi group SKAT test using Liu et al. approximationSKAT.continuous
Multi group SKAT test using bootstrap samplingSKAT.permutations
Multi group SKAT test using Liu et al. approximationSKAT.theoretical
Exemple of functional categoriessubregions.LCT
WSS genetic scoreWSS