# Filtering of coding and non-coding genetic variants

## Documentation for package ‘VariantFiltering’ version 1.30.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D F G H I L M N O P R S T U V W X misc

VariantFiltering-package | Filtering of coding and non-coding genetic variants

## -- A --

allVariants | VariantFilteringResults class
allVariants-method | VariantFilteringResults class
annoGroups | VariantFilteringResults class
annoGroups-method | VariantFilteringResults class
autosomalDominant | Autosomal dominant inheritance analysis
autosomalDominant-method | Autosomal dominant inheritance analysis
autosomalRecessiveHeterozygous | Autosomal recessive inheritance analysis: Heterozygous
autosomalRecessiveHeterozygous-method | Autosomal recessive inheritance analysis: Heterozygous
autosomalRecessiveHomozygous | Autosomal recessive inheritance analysis: Homozygous
autosomalRecessiveHomozygous-method | Autosomal recessive inheritance analysis: Homozygous

## -- B --

bamFiles | VariantFilteringResults class
bamFiles-method | VariantFilteringResults class
bamFiles<- | VariantFilteringResults class
bamFiles<--method | VariantFilteringResults class
browseVariants | VariantFilteringResults class

## -- C --

change | VariantFilteringResults class
change<- | VariantFilteringResults class
change<-,CutoffsList | VariantFilteringResults class
change<--method | VariantFilteringResults class
class:CutoffsList | VariantFilteringResults class
class:VariantFilteringParam | VariantFiltering parameter class
class:VariantFilteringResults | VariantFilteringResults class
conservedPositions | Weight matrix class
conservedPositions-method | Weight matrix class
cutoffs | VariantFilteringResults class
cutoffs-method | VariantFiltering parameter class
cutoffs-method | VariantFilteringResults class
cutoffs<- | VariantFilteringResults class
cutoffs<--method | VariantFilteringResults class
CutoffsList | VariantFilteringResults class
CutoffsList-class | VariantFilteringResults class

## -- D --

deNovo | De Novo variants analysis
deNovo-method | De Novo variants analysis
downstream | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
downstream-method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
downstream<- | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
downstream<--method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType

## -- F --

filteredVariants | VariantFilteringResults class
filteredVariants-method | VariantFilteringResults class
filters | VariantFilteringResults class
filters-method | VariantFiltering parameter class
filters-method | VariantFilteringResults class
filters<- | VariantFilteringResults class
filters<--method | VariantFilteringResults class
filtersMetadata | VariantFilteringResults class
filtersMetadata-method | VariantFilteringResults class
FiveSpliceSiteVariants | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
FiveSpliceSiteVariants-class | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType

## -- G --

genePhylostrata | PhastConsDb class
genePhylostrata-method | PhastConsDb class
GenePhylostrataDb | PhastConsDb class
GenePhylostrataDb-class | PhastConsDb class
genePhylostratum | PhastConsDb class
genePhylostratum-method | PhastConsDb class

## -- H --

humanGenesPhylostrata | PhastConsDb class

## -- I --

inheritanceModel | VariantFilteringResults class
inheritanceModel-method | VariantFilteringResults class

## -- L --

length | VariantFilteringResults class
length-method | VariantFilteringResults class

## -- M --

minIntronLength | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
minIntronLength-method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
minIntronLength<- | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
minIntronLength<--method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType

## -- N --

names-method | VariantFiltering parameter class

## -- O --

organism-method | PhastConsDb class

## -- P --

param | VariantFilteringResults class
param-method | VariantFilteringResults class
plot-method | VariantFilteringResults class

## -- R --

readAAradicalChangeMatrix | Read matrix of amino acid radical changes
readWm | Weight matrix class
referenceGenome-method | VariantFilteringResults class
reportVariants | VariantFilteringResults class
reportVariants-method | VariantFilteringResults class
resetSamples | VariantFilteringResults class
resetSamples-method | VariantFilteringResults class

## -- S --

samples | VariantFilteringResults class
samples-method | VariantFilteringResults class
samples<- | VariantFilteringResults class
samples<--method | VariantFilteringResults class
sequence_variant.gSOXP | VariantFiltering parameter class
show-method | PhastConsDb class
show-method | VariantFiltering parameter class
show-method | VariantFilteringResults class
show-method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
show-method | Weight matrix class
softFilterMatrix-method | VariantFilteringResults class
softFilterMatrix<--method | VariantFilteringResults class
sog | VariantFilteringResults class
sog-method | VariantFiltering parameter class
sog-method | VariantFilteringResults class
sortings | VariantFilteringResults class
sortings-method | VariantFilteringResults class
sortings<- | VariantFilteringResults class
sortings<--method | VariantFilteringResults class
spliceSiteMatricesHuman | VariantFiltering parameter class
summary-method | VariantFilteringResults class

## -- T --

ThreeSpliceSiteVariants | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
ThreeSpliceSiteVariants-class | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType

## -- U --

unrelatedIndividuals | Analysis designed to be applied over a group of unrelated individuals
unrelatedIndividuals-method | Analysis designed to be applied over a group of unrelated individuals
upstream | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
upstream-method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
upstream<- | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType
upstream<--method | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType

## -- V --

VariantFiltering | Filtering of coding and non-coding genetic variants
VariantFilteringParam | VariantFiltering parameter class
VariantFilteringParam-class | VariantFiltering parameter class
VariantFilteringResults | VariantFilteringResults class
VariantFilteringResults-class | VariantFilteringResults class
variantLocations | VariantFiltering parameter class

## -- W --

WeightMatrix | Weight matrix class
WeightMatrix-class | Weight matrix class
width-method | Weight matrix class
wmFilename | Weight matrix class
wmFilename-method | Weight matrix class
wmLocations | Weight matrix class
wmLocations-method | Weight matrix class
wmLocations<- | Weight matrix class
wmLocations<--method | Weight matrix class
wmName | Weight matrix class
wmName-method | Weight matrix class
wmScore | Weight matrix class
wmScore-method | Weight matrix class
wmStrictLocations | Weight matrix class
wmStrictLocations-method | Weight matrix class
wmStrictLocations<- | Weight matrix class
wmStrictLocations<--method | Weight matrix class

## -- X --

xLinked | X-Linked inheritance analysis
xLinked-method | X-Linked inheritance analysis

## -- misc --

$-method | VariantFiltering parameter class