# Filtering of coding and non-coding genetic variants

## Documentation for package ‘VariantFiltering’ version 1.2.14

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

## Help Pages

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