A B C D F G H I K L M N O P R S T U V W X misc
VariantFiltering-package | Filtering of coding and non-coding genetic variants |
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 |
bamFiles | VariantFilteringResults class |
bamFiles-method | VariantFilteringResults class |
bamFiles<- | VariantFilteringResults class |
bamFiles<--method | VariantFilteringResults class |
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 |
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 |
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 |
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 |
genePhylostrata | PhastConsDb class |
genePhylostrata-method | PhastConsDb class |
GenePhylostrataDb | PhastConsDb class |
GenePhylostrataDb-class | PhastConsDb class |
genePhylostratum | PhastConsDb class |
genePhylostratum-method | PhastConsDb class |
humanGenesPhylostrata | PhastConsDb class |
inheritanceModel | VariantFilteringResults class |
inheritanceModel-method | VariantFilteringResults class |
keys | MafDb class |
keys-method | MafDb class |
keytypes | MafDb class |
keytypes-method | MafDb class |
knownVariantsMAFcols | MafDb class |
knownVariantsMAFcols-method | MafDb class |
length | VariantFilteringResults class |
length-method | VariantFilteringResults class |
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 |
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 |
naMAF | VariantFilteringResults class |
naMAF-method | VariantFilteringResults class |
naMAF<- | VariantFilteringResults class |
naMAF<--method | VariantFilteringResults class |
names-method | VariantFiltering parameter class |
OMIMpresent | VariantFilteringResults class |
OMIMpresent-method | VariantFilteringResults class |
OMIMpresent<- | VariantFilteringResults class |
OMIMpresent<--method | VariantFilteringResults class |
organism-method | PhastConsDb class |
organism-method | PhastConsDb class |
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 |
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 |
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 | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
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 |
ThreeSpliceSiteVariants | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
ThreeSpliceSiteVariants-class | FiveSpliceSiteVariants and ThreeSpliceSiteVariants subclasses of VariantType |
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 |
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 |
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 |
xLinked | X-Linked inheritance analysis |
xLinked-method | X-Linked inheritance analysis |
$-method | VariantFiltering parameter class |