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.

Author
Robert Castelo [aut, cre], Dei Martinez Elurbe [ctb], Pau Puigdevall [ctb]
Date of publication
None
Maintainer
Robert Castelo <robert.castelo@upf.edu>
License
Artistic-2.0
Version
1.10.1
URLs

View on Bioconductor

Man pages

autosomalDominant
Autosomal dominant inheritance analysis
autosomalRecessiveHeterozygous
Autosomal recessive inheritance analysis: Heterozygous
autosomalRecessiveHomozygous
Autosomal recessive inheritance analysis: Homozygous
deNovo
De Novo variants analysis
GenePhylostrataDb-class
PhastConsDb class
MafDb2-class
MafDb2 class
MafDb-class
MafDb class
PhastConsDb-class
PhastConsDb class
readAAradicalChangeMatrix
Read matrix of amino acid radical changes
unrelatedIndividuals
Analysis designed to be applied over a group of unrelated...
VariantFiltering-defunct
Defunct functions in package 'VariantFiltering'
VariantFiltering-deprecated
Deprecated functions in package 'VariantFiltering'
VariantFiltering-package
Filtering of coding and non-coding genetic variants
VariantFilteringParam-class
VariantFiltering parameter class
VariantFilteringResults-class
VariantFilteringResults class
VariantType-class
FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses...
WeightMatrix-class
Weight matrix class
xLinked
X-Linked inheritance analysis

Files in this package

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