Filtering of coding and non-coding genetic variants


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Documentation for package ‘VariantFiltering’ version 1.2.14

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

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

-- A --

aaChangeType VariantFiltering results class
aaChangeType-method VariantFiltering results class
aaChangeType<- VariantFiltering results class
aaChangeType<--method VariantFiltering results class
allInheritanceModels Analysis designed to be applied over a group of related individuals
allInheritanceModels-method Analysis designed to be applied over a group of related individuals
allVariants VariantFiltering results class
allVariants-method VariantFiltering results class
annotateVariants MafDb class
annotateVariants-method PhastConsDb class
annotateVariants-method MafDb class
annotateVariants-method PhastConsDb 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

-- C --

class:VariantFilteringParam VariantFiltering parameter class
class:VariantFilteringResults VariantFiltering results class
class:VariantFilteringResultsAIM VariantFiltering results class
class:VariantFilteringResultsUI VariantFiltering results class
codeAF2RAW MafDb class
columns MafDb class
columns-method MafDb class
conservedPositions Weight matrix class
conservedPositions-method Weight matrix class

-- D --

dbSNPpresent VariantFiltering results class
dbSNPpresent-method VariantFiltering results class
dbSNPpresent<- VariantFiltering results class
dbSNPpresent<--method VariantFiltering results class
decodeRAW2AF MafDb class
deNovo De Novo variants analysis
deNovo-method De Novo variants analysis

-- F --

fetchKnownVariantsByID MafDb class
fetchKnownVariantsByID-method MafDb class
filteredVariants VariantFiltering results class
filteredVariants-method VariantFiltering results class

-- 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 VariantFiltering results class
inheritanceModel-method VariantFiltering results class

-- K --

keys MafDb class
keys-method MafDb class
keytypes MafDb class
keytypes-method MafDb class
knownVariantsMAFcols MafDb class
knownVariantsMAFcols-method MafDb class

-- M --

MafDb MafDb class
MafDb-class MafDb class
MAFpop VariantFiltering results class
MAFpop-method VariantFiltering results class
MAFpop<- VariantFiltering results class
MAFpop<--method VariantFiltering results class
maxMAF VariantFiltering results class
maxMAF-method VariantFiltering results class
maxMAF<- VariantFiltering results class
maxMAF<--method VariantFiltering results class
minCRYP3ss VariantFiltering results class
minCRYP3ss-method VariantFiltering results class
minCRYP3ss<- VariantFiltering results class
minCRYP3ss<--method VariantFiltering results class
minCRYP5ss VariantFiltering results class
minCRYP5ss-method VariantFiltering results class
minCRYP5ss<- VariantFiltering results class
minCRYP5ss<--method VariantFiltering results class
minPhastCons VariantFiltering results class
minPhastCons-method VariantFiltering results class
minPhastCons<- VariantFiltering results class
minPhastCons<--method VariantFiltering results class
minPhylostratum VariantFiltering results class
minPhylostratum-method VariantFiltering results class
minPhylostratum<- VariantFiltering results class
minPhylostratum<--method VariantFiltering results class

-- N --

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

-- O --

OMIMpresent VariantFiltering results class
OMIMpresent-method VariantFiltering results class
OMIMpresent<- VariantFiltering results class
OMIMpresent<--method VariantFiltering results class
organism-method PhastConsDb class
organism-method PhastConsDb class

-- P --

param VariantFiltering results class
param-method VariantFiltering results class
PhastConsDb PhastConsDb class
PhastConsDb-class PhastConsDb class
provider-method PhastConsDb class
providerVersion-method PhastConsDb class

-- R --

readAAradicalChangeMatrix Read matrix of amino acid radical changes
readWm Weight matrix class
referenceGenome-method PhastConsDb class
reportVariants VariantFiltering results class
reportVariants-method VariantFiltering results class

-- S --

scores PhastConsDb class
scores-method PhastConsDb class
select MafDb class
select-method MafDb class
selectIndividual VariantFiltering results class
selectIndividual-method VariantFiltering results class
selectIndividual<- VariantFiltering results class
selectIndividual<--method VariantFiltering results class
seqinfo-method PhastConsDb class
seqlengths-method PhastConsDb class
seqnames-method PhastConsDb class
show-method PhastConsDb class
show-method PhastConsDb class
show-method VariantFiltering parameter class
show-method VariantFiltering results class
show-method Weight matrix class

-- 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

-- V --

VariantFiltering Filtering of coding and non-coding genetic variants
VariantFilteringParam VariantFiltering parameter class
VariantFilteringParam-class VariantFiltering parameter class
VariantFilteringParam-method VariantFiltering parameter class
VariantFilteringResults VariantFiltering results class
VariantFilteringResults-class VariantFiltering results class
VariantFilteringResultsAIM VariantFiltering results class
VariantFilteringResultsAIM-class VariantFiltering results class
VariantFilteringResultsUI VariantFiltering results class
VariantFilteringResultsUI-class VariantFiltering results class
variantType VariantFiltering results class
variantType-method VariantFiltering results class
variantType<- VariantFiltering results class
variantType<--method VariantFiltering results class

-- W --

WeightMatrix Weight matrix class
WeightMatrix-class Weight matrix class
width-method Weight matrix class
wmAcceptorSites Weight matrix class
wmDonorSites Weight matrix class
wmScore Weight matrix class
wmScore-method Weight matrix class

-- X --

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

-- misc --

$-method VariantFiltering parameter class