Filtering of coding and non-coding genetic variants


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Documentation for package ‘VariantFiltering’ version 1.42.0

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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