Filtering of coding and non-coding genetic variants


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Documentation for package ‘VariantFiltering’ version 1.4.3

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

VariantFiltering-package 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
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

-- 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
codeAF2RAW MafDb class
columns MafDb class
columns-method MafDb 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
decodeRAW2AF MafDb class
deNovo De Novo variants analysis
deNovo-method De Novo variants analysis

-- 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

-- 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

-- K --

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

-- L --

length VariantFilteringResults class
length-method VariantFilteringResults class

-- M --

MafDb MafDb class
MafDb-class MafDb class
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
minCRYP3ss VariantFilteringResults class
minCRYP3ss-method VariantFilteringResults class
minCRYP3ss<- VariantFilteringResults class
minCRYP3ss<--method VariantFilteringResults class
minCRYP5ss VariantFilteringResults class
minCRYP5ss-method VariantFilteringResults class
minCRYP5ss<- VariantFilteringResults class
minCRYP5ss<--method VariantFilteringResults class
minCUFC VariantFilteringResults class
minCUFC-method VariantFilteringResults class
minCUFC<- VariantFilteringResults class
minCUFC<--method VariantFilteringResults class
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

-- 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
organism-method PhastConsDb class

-- P --

param VariantFilteringResults class
param-method VariantFilteringResults class
PhastConsDb PhastConsDb class
PhastConsDb-class PhastConsDb class
plot-method VariantFilteringResults 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 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
scores PhastConsDb class
scores-method PhastConsDb class
select MafDb class
select-method MafDb class
seqinfo-method PhastConsDb class
seqlengths-method PhastConsDb class
seqnames-method PhastConsDb class
sequence_variant.gSOXP VariantFiltering parameter class
show-method PhastConsDb class
show-method PhastConsDb class
show-method VariantFiltering parameter class
show-method VariantFilteringResults class
show-method Weight matrix class
snpid2maf MafDb class
snpid2maf-method MafDb class
softFilterMatrix-method VariantFilteringResults class
softFilterMatrix<--method VariantFilteringResults class
sog VariantFilteringResults class
sog-method VariantFiltering parameter class
sog-method VariantFilteringResults class
spliceSiteMatricesHsapiens VariantFiltering parameter class
spliceSiteMatricesHuman VariantFiltering parameter class
summary-method VariantFilteringResults 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 --

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
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
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