Filtering of coding and non-coding genetic variants

Documentation for package ‘VariantFiltering’ version 1.14.0

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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

Filtering of coding and non-coding genetic variants

-- A --

aaChangeType	VariantFilteringResults class
aaChangeType-method	VariantFilteringResults class
aaChangeType<-	VariantFilteringResults class
aaChangeType<--method	VariantFilteringResults class
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

-- C --

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

-- D --

dbSNPpresent	VariantFilteringResults class
dbSNPpresent-method	VariantFilteringResults class
dbSNPpresent<-	VariantFilteringResults class
dbSNPpresent<--method	VariantFilteringResults class
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
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 --

MAFpop	VariantFilteringResults class
MAFpop-method	VariantFilteringResults class
MAFpop<-	VariantFilteringResults class
MAFpop<--method	VariantFilteringResults class
maxMAF	VariantFilteringResults class
maxMAF-method	VariantFilteringResults class
maxMAF<-	VariantFilteringResults class
maxMAF<--method	VariantFilteringResults class
minCUFC	VariantFilteringResults class
minCUFC-method	VariantFilteringResults class
minCUFC<-	VariantFilteringResults class
minCUFC<--method	VariantFilteringResults class
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
minPhastCons	VariantFilteringResults class
minPhastCons-method	VariantFilteringResults class
minPhastCons<-	VariantFilteringResults class
minPhastCons<--method	VariantFilteringResults class
minPhylostratum	VariantFilteringResults class
minPhylostratum-method	VariantFilteringResults class
minPhylostratum<-	VariantFilteringResults class
minPhylostratum<--method	VariantFilteringResults class
minScore3ss	VariantFilteringResults class
minScore3ss-method	VariantFilteringResults class
minScore3ss<-	VariantFilteringResults class
minScore3ss<--method	VariantFilteringResults class
minScore5ss	VariantFilteringResults class
minScore5ss-method	VariantFilteringResults class
minScore5ss<-	VariantFilteringResults class
minScore5ss<--method	VariantFilteringResults class

-- N --

naMAF	VariantFilteringResults class
naMAF-method	VariantFilteringResults class
naMAF<-	VariantFilteringResults class
naMAF<--method	VariantFilteringResults class
names-method	VariantFiltering parameter class

-- O --

OMIMpresent	VariantFilteringResults class
OMIMpresent-method	VariantFilteringResults class
OMIMpresent<-	VariantFilteringResults class
OMIMpresent<--method	VariantFilteringResults class
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
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 --

variantConsequence	VariantFilteringResults class
variantConsequence-method	VariantFilteringResults class
variantConsequence<-	VariantFilteringResults class
variantConsequence<--method	VariantFilteringResults class
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
variantLocation	VariantFilteringResults class
variantLocation-method	VariantFilteringResults class
variantLocation<-	VariantFilteringResults class
variantLocation<--method	VariantFilteringResults class
variantLocations	VariantFiltering parameter class
variantType	VariantFilteringResults class
variantType-method	VariantFilteringResults class
variantType<-	VariantFilteringResults class
variantType<--method	VariantFilteringResults 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