VariantFiltering: Filtering of coding and non-coding genetic variants

Filter genetic variants using different criteria such as inheritance model, amino acid change consequence, minor allele frequencies across human populations, splice site strength, conservation, etc.

AuthorRobert Castelo [aut, cre], Dei Martinez Elurbe [ctb], Pau Puigdevall [ctb]
Date of publicationNone
MaintainerRobert Castelo <robert.castelo@upf.edu>
LicenseArtistic-2.0
Version1.10.1
https://github.com/rcastelo/VariantFiltering

View on Bioconductor

Functions

aaChangeType Man page
aaChangeType<- Man page
aaChangeType<-,VariantFilteringResults,character-method Man page
aaChangeType,VariantFilteringResults-method Man page
allVariants Man page
allVariants,VariantFilteringResults-method Man page
annotateVariants Man page
annotateVariants,GenePhylostrataDb-method Man page
annotateVariants,MafDb2-method Man page
annotateVariants,MafDb-method Man page
annotateVariants,OrgDb-method Man page
annotateVariants,PhastConsDb-method Man page
annotateVariants,PolyPhenDb-method Man page
annotateVariants,PROVEANDb-method Man page
annotateVariants,SNPlocs-method Man page
annotateVariants,TxDb-method Man page
annotateVariants,XtraSNPlocs-method Man page
autosomalDominant Man page
autosomalDominant,VariantFilteringParam-method Man page
autosomalRecessiveHeterozygous Man page
autosomalRecessiveHeterozygous,VariantFilteringParam-method Man page
autosomalRecessiveHomozygous Man page
autosomalRecessiveHomozygous,VariantFilteringParam-method Man page
bamFiles Man page
bamFiles<- Man page
bamFiles<-,VariantFilteringResults,BamViews-method Man page
bamFiles<-,VariantFilteringResults-method Man page
bamFiles,VariantFilteringResults-method Man page
class:VariantFilteringParam Man page
class:VariantFilteringResults Man page
codeAF2RAW Man page
codeAF2RAW Man page
columns Man page
columns Man page
columns,MafDb2-method Man page
columns,MafDb-method Man page
conservedPositions Man page
conservedPositions,WeightMatrix-method Man page
cutoffs Man page
cutoffs<- Man page
cutoffs,VariantFilteringParam-method Man page
cutoffs<-,VariantFilteringResults-method Man page
cutoffs,VariantFilteringResults-method Man page
dbSNPpresent Man page
dbSNPpresent<- Man page
dbSNPpresent<-,VariantFilteringResults,ANY-method Man page
dbSNPpresent<-,VariantFilteringResults-method Man page
dbSNPpresent,VariantFilteringResults-method Man page
decodeRAW2AF Man page
decodeRAW2AF Man page
deNovo Man page
deNovo,VariantFilteringParam-method Man page
downstream Man page
downstream<- Man page
downstream<-,FiveSpliceSiteVariants-method Man page
downstream,FiveSpliceSiteVariants-method Man page
downstream<-,ThreeSpliceSiteVariants-method Man page
downstream,ThreeSpliceSiteVariants-method Man page
fetchKnownVariantsByID Man page
fetchKnownVariantsByID,MafDb-method Man page
filteredVariants Man page
filteredVariants,VariantFilteringResults-method Man page
filters Man page
filters<- Man page
filters,VariantFilteringParam-method Man page
filters<-,VariantFilteringResults-method Man page
filters,VariantFilteringResults-method Man page
FiveSpliceSiteVariants Man page
FiveSpliceSiteVariants-class Man page
genePhylostrata Man page
GenePhylostrataDb Man page
GenePhylostrataDb Man page
GenePhylostrataDb-class Man page
genePhylostrata,GenePhylostrataDb-method Man page
genePhylostratum Man page
genePhylostratum,GenePhylostrataDb,character-method Man page
genePhylostratum,GenePhylostrataDb-method Man page
genePhylostratum,GenePhylostrataDb,missing-method Man page
humanGenesPhylostrata Man page
inheritanceModel Man page
inheritanceModel,VariantFilteringResults-method Man page
keys Man page
keys Man page
keys,MafDb2-method Man page
keys,MafDb-method Man page
keytypes Man page
keytypes Man page
keytypes,MafDb2-method Man page
keytypes,MafDb-method Man page
knownVariantsMAFcols Man page
knownVariantsMAFcols,MafDb-method Man page
length Man page
length,VariantFilteringResults-method Man page
mafById Man page
mafById,MafDb2-method Man page
mafByOverlaps Man page
mafByOverlaps,MafDb2-method Man page
MafDb Man page
MafDb2 Man page
MafDb2-class Man page
$,MafDb2-method Man page
MafDb-class Man page
MAFpop Man page
MAFpop<- Man page
MAFpop<-,VariantFilteringResults,ANY,logical-method Man page
MAFpop<-,VariantFilteringResults,logical-method Man page
MAFpop<-,VariantFilteringResults-method Man page
MAFpop,VariantFilteringResults-method Man page
maxMAF Man page
maxMAF<- Man page
maxMAF,VariantFilteringResults-method Man page
maxMAF<-,VariantFilteringResults,numeric-method Man page
minCUFC Man page
minCUFC<- Man page
minCUFC,VariantFilteringResults-method Man page
minCUFC<-,VariantFilteringResults,numeric-method Man page
minIntronLength Man page
minIntronLength<- Man page
minIntronLength<-,FiveSpliceSiteVariants-method Man page
minIntronLength,FiveSpliceSiteVariants-method Man page
minIntronLength<-,ThreeSpliceSiteVariants-method Man page
minIntronLength,ThreeSpliceSiteVariants-method Man page
minPhastCons Man page
minPhastCons<- Man page
minPhastCons<-,VariantFilteringResults,ANY-method Man page
minPhastCons<-,VariantFilteringResults-method Man page
minPhastCons,VariantFilteringResults-method Man page
minPhylostratum Man page
minPhylostratum<- Man page
minPhylostratum<-,VariantFilteringResults,ANY-method Man page
minPhylostratum<-,VariantFilteringResults-method Man page
minPhylostratum,VariantFilteringResults-method Man page
minScore3ss Man page
minScore3ss<- Man page
minScore3ss<-,VariantFilteringResults,ANY-method Man page
minScore3ss<-,VariantFilteringResults-method Man page
minScore3ss,VariantFilteringResults-method Man page
minScore5ss Man page
minScore5ss<- Man page
minScore5ss<-,VariantFilteringResults,ANY-method Man page
minScore5ss<-,VariantFilteringResults-method Man page
minScore5ss,VariantFilteringResults-method Man page
naMAF Man page
naMAF<- Man page
naMAF<-,VariantFilteringResults,logical-method Man page
naMAF,VariantFilteringResults-method Man page
names,VariantFilteringParam-method Man page
OMIMpresent Man page
OMIMpresent<- Man page
OMIMpresent<-,VariantFilteringResults,character-method Man page
OMIMpresent<-,VariantFilteringResults-method Man page
OMIMpresent,VariantFilteringResults-method Man page
organism,GenePhylostrataDb-method Man page
organism,MafDb2-method Man page
organism,PhastConsDb-method Man page
param Man page
param,VariantFilteringResults-method Man page
PhastConsDb Man page
PhastConsDb Man page
PhastConsDb-class Man page
plot,VariantFilteringResults,ANY-method Man page
populations Man page
populations,MafDb2-method Man page
provider,MafDb2-method Man page
provider,PhastConsDb-method Man page
providerVersion,MafDb2-method Man page
providerVersion,PhastConsDb-method Man page
readAAradicalChangeMatrix Man page
readWm Man page
referenceGenome,MafDb2-method Man page
referenceGenome,PhastConsDb-method Man page
reportVariants Man page
reportVariants,VariantFilteringResults-method Man page
resetSamples Man page
resetSamples,VariantFilteringResults-method Man page
samples Man page
samples<- Man page
samples<-,VariantFilteringResults,character-method Man page
samples<-,VariantFilteringResults-method Man page
samples,VariantFilteringResults-method Man page
scores Man page
scores,PhastConsDb,GRanges-method Man page
select Man page
select Man page
select,MafDb2-method Man page
select,MafDb-method Man page
seqinfo,MafDb2-method Man page
seqinfo,PhastConsDb-method Man page
seqlengths,MafDb2-method Man page
seqlengths,PhastConsDb-method Man page
seqlevelsStyle,MafDb2-method Man page
seqlevelsStyle,PhastConsDb-method Man page
seqnames,MafDb2-method Man page
seqnames,PhastConsDb-method Man page
sequence_variant.gSOXP Man page
show,CompressedVRangesList-method Man page
show,FiveSpliceSiteVariants-method Man page
show,GenePhylostrataDb-method Man page
show,MafDb2-method Man page
show,PhastConsDb-method Man page
show,ThreeSpliceSiteVariants-method Man page
show,VariantFilteringParam-method Man page
show,VariantFilteringResults-method Man page
show,VariantFilteringResultsUI-method Man page
show,WeightMatrix-method Man page
snpid2maf Man page
snpid2maf,MafDb-method Man page
softFilterMatrix<-,VariantFilteringResults-method Man page
softFilterMatrix,VariantFilteringResults-method Man page
sog Man page
sog,VariantFilteringParam-method Man page
sog,VariantFilteringResults-method Man page
spliceSiteMatricesHuman Man page
summary,VariantFilteringResults-method Man page
ThreeSpliceSiteVariants Man page
ThreeSpliceSiteVariants-class Man page
unrelatedIndividuals Man page
unrelatedIndividuals,VariantFilteringParam-method Man page
upstream Man page
upstream<- Man page
upstream<-,FiveSpliceSiteVariants-method Man page
upstream,FiveSpliceSiteVariants-method Man page
upstream<-,ThreeSpliceSiteVariants-method Man page
upstream,ThreeSpliceSiteVariants-method Man page
variantConsequence Man page
variantConsequence<- Man page
variantConsequence<-,VariantFilteringResults,ANY,logical-method Man page
variantConsequence<-,VariantFilteringResults,logical-method Man page
variantConsequence<-,VariantFilteringResults-method Man page
variantConsequence,VariantFilteringResults-method Man page
VariantFiltering Man page
VariantFiltering-defunct Man page
VariantFiltering-deprecated Man page
VariantFiltering-package Man page
VariantFilteringParam Man page
VariantFilteringParam-class Man page
$,VariantFilteringParam-method Man page
VariantFilteringResults Man page
VariantFilteringResults-class Man page
variantLocation Man page
variantLocation<- Man page
variantLocations Man page
variantLocation<-,VariantFilteringResults,ANY,logical-method Man page
variantLocation<-,VariantFilteringResults,logical-method Man page
variantLocation<-,VariantFilteringResults-method Man page
variantLocation,VariantFilteringResults-method Man page
variantType Man page
variantType<- Man page
variantType<-,VariantFilteringResults,ANY,logical-method Man page
variantType<-,VariantFilteringResults,logical-method Man page
variantType<-,VariantFilteringResults-method Man page
variantType,VariantFilteringResults-method Man page
WeightMatrix Man page
WeightMatrix-class Man page
width,WeightMatrix-method Man page
wmFilename Man page
wmFilename,WeightMatrix-method Man page
wmLocations Man page
wmLocations<- Man page
wmLocations<-,WeightMatrix,character-method Man page
wmLocations<-,WeightMatrix-method Man page
wmLocations,WeightMatrix-method Man page
wmName Man page
wmName,WeightMatrix-method Man page
wmScore Man page
wmScore,character,character-method Man page
wmScore,character,DNAStringSet-method Man page
wmScore,WeightMatrix,character-method Man page
wmScore,WeightMatrix,DNAStringSet-method Man page
wmStrictLocations Man page
wmStrictLocations<- Man page
wmStrictLocations<-,WeightMatrix,logical-method Man page
wmStrictLocations<-,WeightMatrix-method Man page
wmStrictLocations,WeightMatrix-method Man page
xLinked Man page
xLinked,VariantFilteringParam-method Man page

Files

VariantFiltering/DESCRIPTION
VariantFiltering/NAMESPACE
VariantFiltering/NEWS
VariantFiltering/R
VariantFiltering/R/AllClasses.R VariantFiltering/R/AllGeneric.R VariantFiltering/R/AllUtilities.R VariantFiltering/R/annotationEngine.R VariantFiltering/R/autosomalDominant.R VariantFiltering/R/autosomalRecessiveHeterozygous.R VariantFiltering/R/autosomalRecessiveHomozygous.R VariantFiltering/R/deNovo.R VariantFiltering/R/defaultFilters.R VariantFiltering/R/methods-GenePhyloStrataDb.R VariantFiltering/R/methods-MafDb.R VariantFiltering/R/methods-MafDb2.R VariantFiltering/R/methods-PhastConsDb.R VariantFiltering/R/methods-SequenceOntology.R VariantFiltering/R/methods-VariantFilteringParam.R VariantFiltering/R/methods-VariantFilteringResults.R VariantFiltering/R/methods-VariantType-class.R VariantFiltering/R/methods-Visualization.R VariantFiltering/R/methods-WeightMatrix.R VariantFiltering/R/methods-locateVariants.R VariantFiltering/R/scoreBindingSiteVariants.R VariantFiltering/R/tabPanelAbout.R VariantFiltering/R/unrelatedIndividuals.R VariantFiltering/R/xLinked.R VariantFiltering/R/zzz.R
VariantFiltering/build
VariantFiltering/build/vignette.rds
VariantFiltering/inst
VariantFiltering/inst/CITATION
VariantFiltering/inst/doc
VariantFiltering/inst/doc/usingVariantFiltering.R
VariantFiltering/inst/doc/usingVariantFiltering.Rnw
VariantFiltering/inst/doc/usingVariantFiltering.pdf
VariantFiltering/inst/extdata
VariantFiltering/inst/extdata/AA_chemical_properties_HanadaGojoboriLi2006.tsv
VariantFiltering/inst/extdata/CEUtrio.ped
VariantFiltering/inst/extdata/CEUtrio.vcf.bgz
VariantFiltering/inst/extdata/CEUtrio.vcf.bgz.tbi
VariantFiltering/inst/extdata/NA12878.subset.bam
VariantFiltering/inst/extdata/NA12878.subset.bam.bai
VariantFiltering/inst/extdata/NA12891.subset.bam
VariantFiltering/inst/extdata/NA12891.subset.bam.bai
VariantFiltering/inst/extdata/NA12892.subset.bam
VariantFiltering/inst/extdata/NA12892.subset.bam.bai
VariantFiltering/inst/extdata/README_SequenceOntology
VariantFiltering/inst/extdata/README_humanGenesPhylostrata
VariantFiltering/inst/extdata/hsap.acceptors.hcmc10_15_1.ibn
VariantFiltering/inst/extdata/hsap.donors.hcmc10_15_1.ibn
VariantFiltering/inst/extdata/humanCodonUsage.txt
VariantFiltering/inst/extdata/humanEnsGenePhylostrata.rda
VariantFiltering/inst/extdata/sequence_variant.gSOXPapril2016.rds
VariantFiltering/inst/extdata/uind.rds
VariantFiltering/inst/unitTests
VariantFiltering/inst/unitTests/test_VariantFilteringParam-methods.R
VariantFiltering/inst/unitTests/test_inheritance-models.R
VariantFiltering/inst/unitTests/test_location-methods.R
VariantFiltering/man
VariantFiltering/man/GenePhylostrataDb-class.Rd VariantFiltering/man/MafDb-class.Rd VariantFiltering/man/MafDb2-class.Rd VariantFiltering/man/PhastConsDb-class.Rd VariantFiltering/man/VariantFiltering-defunct.Rd VariantFiltering/man/VariantFiltering-deprecated.Rd VariantFiltering/man/VariantFiltering-package.Rd VariantFiltering/man/VariantFilteringParam-class.Rd VariantFiltering/man/VariantFilteringResults-class.Rd VariantFiltering/man/VariantType-class.Rd VariantFiltering/man/WeightMatrix-class.Rd VariantFiltering/man/autosomalDominant.Rd VariantFiltering/man/autosomalRecessiveHeterozygous.Rd VariantFiltering/man/autosomalRecessiveHomozygous.Rd VariantFiltering/man/deNovo.Rd VariantFiltering/man/readAAradicalChangeMatrix.Rd VariantFiltering/man/unrelatedIndividuals.Rd VariantFiltering/man/xLinked.Rd
VariantFiltering/src
VariantFiltering/src/Biostrings_stubs.c
VariantFiltering/src/R_init_VariantFiltering.c
VariantFiltering/src/VariantFiltering.h
VariantFiltering/src/methods-WeightMatrix.c
VariantFiltering/tests
VariantFiltering/tests/runTests.R
VariantFiltering/vignettes
VariantFiltering/vignettes/shinysnapshotVariantFiltering.jpg
VariantFiltering/vignettes/usingVariantFiltering.Rnw

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