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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("VariantFiltering")
AuthorRobert Castelo [aut, cre], Dei Martinez Elurbe [ctb], Pau Puigdevall [ctb]
Bioconductor views Annotation Genetics HighThroughputSequencing Homo_sapiens SNP Sequencing
Date of publicationNone
MaintainerRobert Castelo <robert.castelo@upf.edu>
LicenseArtistic-2.0
Version1.12.0
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,GScores-method Man page
annotateVariants,MafDb2-method Man page
annotateVariants,MafDb-method Man page
annotateVariants,OrgDb-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
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
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
length Man page
length,VariantFilteringResults-method Man page
mafById Man page
mafById Man page
mafById,MafDb2-method Man page
mafById,MafDb-method Man page
mafByOverlaps Man page
mafByOverlaps Man page
mafByOverlaps,MafDb2-method Man page
mafByOverlaps,MafDb-method Man page
MafDb Man page
MafDb2 Man page
MafDb2-class Man page
$,MafDb2-method Man page
MafDb-class Man page
$,MafDb-method 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,MafDb-method Man page
param Man page
param,VariantFilteringResults-method Man page
plot,VariantFilteringResults,ANY-method Man page
populations Man page
populations Man page
populations,MafDb2-method Man page
populations,MafDb-method Man page
provider,MafDb2-method Man page
provider,MafDb-method Man page
providerVersion,MafDb2-method Man page
providerVersion,MafDb-method Man page
readAAradicalChangeMatrix Man page
readWm Man page
referenceGenome,MafDb2-method Man page
referenceGenome,MafDb-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
seqinfo,MafDb2-method Man page
seqinfo,MafDb-method Man page
seqlengths,MafDb2-method Man page
seqlengths,MafDb-method Man page
seqlevelsStyle,MafDb2-method Man page
seqlevelsStyle,MafDb-method Man page
seqnames,MafDb2-method Man page
seqnames,MafDb-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,MafDb-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
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

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

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