pappewaio/AllelicImbalance
Investigates Allele Specific Expression

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Search the pappewaio/AllelicImbalance package
Vignettes
Functions
343
Source code
50
Man pages
71
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pappewaio/AllelicImbalance: Investigates Allele Specific Expression
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API

API for pappewaio/AllelicImbalance
Investigates Allele Specific Expression

Global functions
.IRangesFromIntegerList Source code
.Na2False Source code
.addLva2ASEset Source code
.aiRegionDirectionFromMaternalPhaseMapBiasAndIndex Source code
.array2MatrixList Source code
.arrayFromAlleleVector Source code
.calcFrequencyFromAlleleCounts Source code
.deltaFromFractionMatrixAndMapBias Source code
.expandMatrixToArray Source code
.genotypeArray2genotypeMatrix Source code
.groupBasedOnPhaseAndAlleleCombination Source code
.heterozygozityFromPhaseArray Source code
.list.depth Source code
.lvaGroups Source code
.lvaRegressionPvalue Source code
.lvaRegressionReturnCommonParamMatrix Source code
.lvaRegressionReturnCommonParamMatrix.nlme Source code
.lvaRegressionReturnCommonParamMatrixTxSNPspecific Source code
.lvaRegressionReturnCommonParamMatrixTxSNPspecific.nlme Source code
.makeMetaASEsetDataFrameForRegionSummary Source code
.makeRegionGRangesFromASEsetWithRegionIndex Source code
.maternalPhaseMapBias Source code
.matrixFromLmListCommonParam Source code
.mergeDirAndFilename Source code
.mergePhaseArray2phaseMatrix Source code
.minusStrandCountsExists Source code
.multiUnlist Source code
.multiUnlist.index Source code
.multiUnlist.index.names Source code
.phaseArray2genotypeArray Source code
.plusStrandCountsExists Source code
.region.list.populate Source code
.regionStatisticsFromMatrixAndIndex Source code
.returnMaternalPhaseFrequency Source code
.selectRegionAndTransferIndexToASEset Source code
.splitGenotypeCount Source code
.splitGenotypeMatrix Source code
.splitGenotypePickAltAllele Source code
.splitGenotypePickRefAllele Source code
.splitGenotypeRank Source code
.subsetArrayToMatrix Source code
.toKeepMatrixMinCountFilterAll Source code
.toKeepMatrixMinCountFilterEach Source code
.toKeepMatrixMinFreqFilterAll Source code
.toKeepMatrixMinFreqFilterEach Source code
.unknownStrandCountsExists Source code
.unlistGRangesListAndIndex Source code
.verboseCoerceToCharacter Source code
ASEDAnnotationTrack Man page
ASEDAnnotationTrack,ASEset-method Man page
ASEset Man page
ASEset-barplot Man page
ASEset-class Man page
ASEset-filters Man page
ASEset-gbarplot Man page
ASEset-glocationplot Man page
ASEset-gviztrack Man page
ASEset-locationplot Man page
ASEset-scanForHeterozygotes Man page
ASEset.old Man page
ASEset.sim Man page
ASEsetFromArrays Man page Source code
ASEsetFromBam Man page
ASEsetFromBam,GRanges-method Man page
ASEsetFromCountList Man page Source code
AllelicImbalance Man page
AllelicImbalance-package Man page
CoverageDataTrack Man page
CoverageDataTrack,ASEset-method Man page
DetectedAI Man page
DetectedAI-class Man page
DetectedAI-method Man page
DetectedAI-plot Man page
DetectedAI-summary Man page
DetectedAIFromArray Man page Source code
GAnalysis Man page Source code
GRvariants Man page
GlobalAnalysis Man page
GlobalAnalysis-class Man page
GlobalAnalysis-method Man page
LinkVariantAlmlof Man page
LinkVariantAlmlof-class Man page
LinkVariantAlmlof-method Man page
LinkVariantAlmlof-plot Man page
RegionSummary Man page
RegionSummary-class Man page
RegionSummary-method Man page
RiskVariant Man page
RiskVariant-class Man page
RiskVariant-method Man page
RiskVariantFromGRangesAndPhaseArray Man page Source code
alleleCounts Man page
alleleCounts,ASEset-method Man page
alleleCounts<- Man page
alleleCounts<-,ASEset-method Man page
alt Man page
alt,ASEset-method Man page
alt,RiskVariant-method Man page
alt<- Man page
alt<-,ASEset,ANY-method Man page
alt<-,RiskVariant,ANY-method Man page
altExist Man page
altExist,ASEset-method Man page
annotation-wrappers Man page
annotationBarplot Man page Source code
aquals Man page
aquals,ASEset-method Man page
aquals<- Man page
aquals<-,ASEset-method Man page
arank Man page
arank,ASEset-method Man page
barplot Man page
barplot,ASEset-method Man page
barplot-lattice-support Man page
barplotLatticeCounts Man page Source code
barplotLatticeFraction Man page Source code Source code
basic Man page
basic,RegionSummary-method Man page
binom.test Man page
binom.test,ASEset-method Man page
chisq.test Man page
chisq.test,ASEset-method Man page
cigar-utilities Man page
countAllelesFromBam Man page
countAllelesFromBam,GRanges-method Man page
countsPerSample Man page
countsPerSample,ASEset-method Man page
countsPerSnp Man page
countsPerSnp,ASEset-method Man page
coverageMatrixListFromGAL Man page
coverageMatrixListFromGAL,GAlignmentsList-method Man page
decorateWithExons Man page Source code
decorateWithGenes Man page Source code
defaultMapBias Man page
defaultMapBias,ASEset-method Man page
defaultPhase Man page
defaultPhase,numeric-method Man page
detectAI Man page
detectAI,ASEset-method Man page
detectedAI_vs_threshold_variable_multigraph_plot Man page
detectedAI_vs_threshold_variable_multigraph_plot,DetectedAI-meth Man page
detectedAI_vs_threshold_variable_plot Man page
detectedAI_vs_threshold_variable_plot,DetectedAI-method Man page
detectedAI_vs_threshold_variable_summary Man page
detectedAI_vs_threshold_variable_summary,DetectedAI-method Man page
fraction Man page
fraction,ASEset-method Man page
fractionPlotDf Man page
fractionPlotDf,ASEset-method Man page
frequency Man page
frequency,ASEset-method Man page
frequency_vs_threshold_variable_multigraph_plot Man page
frequency_vs_threshold_variable_multigraph_plot,DetectedAI-metho Man page
frequency_vs_threshold_variable_plot Man page
frequency_vs_threshold_variable_plot,DetectedAI-class Man page
frequency_vs_threshold_variable_plot,DetectedAI-method Man page
frequency_vs_threshold_variable_summary Man page
frequency_vs_threshold_variable_summary,DetectedAI-method Man page
gba Man page
gba,character-method Man page
gbarplot Man page
gbarplot,ASEset-method Man page
genomatrix Man page
genotype Man page
genotype,ASEset-method Man page
genotype2phase Man page
genotype2phase,matrix-method Man page
genotype<- Man page
genotype<-,ASEset-method Man page
getAlleleCount Source code
getAlleleCounts Man page
getAlleleCounts,GAlignmentsList-method Man page
getAlleleQuality Man page
getAlleleQuality,GAlignmentsList-method Man page
getAnnotationDataFrame Man page Source code
getAreaFromGeneNames Man page
getAreaFromGeneNames,character-method Man page
getCDSFromAnnotation Man page Source code
getCDSVector Man page Source code
getDefaultMapBiasExpMean Man page
getDefaultMapBiasExpMean,ANY-method Man page
getDefaultMapBiasExpMean,list-method Man page
getDefaultMapBiasExpMean3D Man page
getDefaultMapBiasExpMean3D,ANY-method Man page
getExonsFromAnnotation Man page Source code
getExonsVector Man page Source code
getGenesFromAnnotation Man page Source code
getGenesVector Man page Source code
getSnpIdFromLocation Man page
getSnpIdFromLocation,GRanges-method Man page
getTranscriptsFromAnnotation Man page Source code
getTranscriptsVector Man page Source code
glocationplot Man page
glocationplot,ASEset-method Man page
hetFilt Man page
hetFilt,ASEset-method Man page
hist Man page
hist,ASEset-method Man page
hist,ReferenceBias-method Man page
histplot Man page
impBamGAL Man page
impBamGAL,character-method Man page
impBamGRL Man page Source code
impBamGRL.old Man page Source code
impBcfGR Man page
impBcfGR,character-method Man page
impBcfGRL Man page
impBcfGRL,character-method Man page
implodeList Source code
implodeList.old Man page Source code
import-bam Man page
import-bam-2 Man page
import-bcf Man page
inferAlleles Man page
inferAlleles,ASEset-method Man page
inferAltAllele Man page
inferAltAllele,ASEset-method Man page
inferGenotypes Man page
inferGenotypes,ASEset-method Man page
initialize-ASEset Man page
initialize-DetectedAI Man page
initialize-GlobalAnalysis Man page
initialize-RiskVariant Man page
legendBarplot Man page Source code
locationplot Man page
locationplot,ASEset-method Man page
lva Man page
lva,ASEset-method Man page
lva,array-method Man page
lva.internal Man page
lva.internal,array-method Man page
makeMaskedFasta Man page
makeMaskedFasta,character-method Man page
mapBias Man page
mapBias,ASEset-method Man page
mapBias<- Man page
mapBias<-,ASEset-method Man page
mapBiasRef Man page
mapBiasRef,ASEset-method Man page
maternalAllele Man page
maternalAllele,ASEset-method Man page
minCountFilt Man page
minCountFilt,ASEset-method Man page
minFreqFilt Man page
minFreqFilt,ASEset-method Man page
minfreqFilt Man page
multiAllelicFilt Man page
multiAllelicFilt,ASEset-method Man page
paternalAllele Man page
paternalAllele,ASEset-method Man page
phase Man page
phase,ASEset-method Man page
phase,RiskVariant-method Man page
phase2genotype Man page
phase2genotype,array-method Man page
phase<- Man page
phase<-,ASEset-method Man page
phase<-,RiskVariant-method Man page
phaseArray2phaseMatrix Man page
phaseArray2phaseMatrix,array-method Man page
phaseMatrix2Array Man page
phaseMatrix2Array,matrix-method Man page
pickSecondMostExpressedAllele Source code
plot Man page
plot,LinkVariantAlmlof,ANY-method Man page
plot,LinkVariantAlmlof-method Man page
pvalue Man page
pvalue,LinkVariantAlmlof-method Man page
randomRef Man page
randomRef,ASEset-method Man page
reads Man page
realCigarPosition Man page Source code
realCigarPosition.old Man page Source code
realCigarPositions Man page Source code
realCigarPositions.old Man page Source code
realCigarPositionsList Man page Source code
realCigarPositionsList.old Man page Source code
ref Man page
ref,ASEset-method Man page
ref,RiskVariant-method Man page
ref<- Man page
ref<-,ASEset,ANY-method Man page
ref<-,RiskVariant,ANY-method Man page
refAllele Man page
refAllele,ASEset-method Man page
refExist Man page
refExist,ASEset-method Man page
referenceFrequency Man page
referenceFrequency,DetectedAI-method Man page
reference_frequency_density_vs_threshold_variable_multigraph_plo Man page Man page
reference_frequency_density_vs_threshold_variable_plot Man page
reference_frequency_density_vs_threshold_variable_plot,DetectedA Man page
regionSummary Man page
regionSummary,ASEset-method Man page
regionSummary,numeric-method Man page
scanForHeterozygotes Man page
scanForHeterozygotes,ASEset-method Man page
scanForHeterozygotes,GAlignmentsList-method Man page
scanForHeterozygotes.old Man page Source code
sumnames Man page
sumnames,RegionSummary-method Man page
thresholdCountSample Man page
thresholdCountSample,DetectedAI-method Man page
thresholdDeltaFrequency Man page
thresholdDeltaFrequency,DetectedAI-method Man page
thresholdFrequency Man page
thresholdFrequency,DetectedAI-method Man page
thresholdPvalue Man page
thresholdPvalue,DetectedAI-method Man page
usedSNPs_vs_threshold_variable_summary Man page
usedSNPs_vs_threshold_variable_summary,DetectedAI-method Man page
pappewaio/AllelicImbalance documentation built on April 11, 2020, 2:58 a.m.

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