Investigates Allele Specific Expression


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Documentation for package ‘AllelicImbalance’ version 1.34.0

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A B C D F G H I L M P R S T U

AllelicImbalance-package A package meant to provide all basic functions for high-throughput allele specific expression analysis

-- A --

alleleCounts ASEset objects
alleleCounts-method ASEset objects
alleleCounts<- ASEset objects
alleleCounts<--method ASEset objects
AllelicImbalance A package meant to provide all basic functions for high-throughput allele specific expression analysis
alt ASEset objects
alt-method ASEset objects
alt-method RiskVariant class
alt<- ASEset objects
alt<--method ASEset objects
alt<--method RiskVariant class
altExist ASEset objects
altExist-method ASEset objects
annotation-wrappers AnnotationDb wrappers
annotationBarplot add annotation to AllelicImbalance barplot
aquals ASEset objects
aquals-method ASEset objects
aquals<- ASEset objects
aquals<--method ASEset objects
arank ASEset objects
arank-method ASEset objects
ASEDAnnotationTrack ASEset-gviztrack ASEset objects
ASEDAnnotationTrack-method ASEset-gviztrack ASEset objects
ASEset ASEset objects
ASEset-barplot barplot ASEset objects
ASEset-class ASEset objects
ASEset-filters genotype filter methods
ASEset-gbarplot gbarplot ASEset objects
ASEset-glocationplot glocationplot ASEset objects
ASEset-gviztrack ASEset-gviztrack ASEset objects
ASEset-locationplot locationplot ASEset objects
ASEset-scanForHeterozygotes scanForHeterozygotes
ASEset.old ASEset.old object
ASEset.sim ASEset.sim object
ASEsetFromArrays Initialize ASEset
ASEsetFromBam ASEset from bam file
ASEsetFromBam-method ASEset from bam file
ASEsetFromCountList Initialize ASEset

-- B --

barplot barplot ASEset objects
barplot-lattice-support lattice barplot inner functions for ASEset objects
barplot-method barplot ASEset objects
barplotLatticeCounts lattice barplot inner functions for ASEset objects
barplotLatticeFraction lattice barplot inner functions for ASEset objects
basic RegionSummary class
basic-method RegionSummary class
binom.test binomial test
binom.test-method binomial test

-- C --

chisq.test chi-square test
chisq.test-method chi-square test
countAllelesFromBam alleleCounts from bam file
countAllelesFromBam-method alleleCounts from bam file
countsPerSample ASEset objects
countsPerSample-method ASEset objects
countsPerSnp ASEset objects
countsPerSnp-method ASEset objects
CoverageDataTrack ASEset-gviztrack ASEset objects
CoverageDataTrack-method ASEset-gviztrack ASEset objects
coverageMatrixListFromGAL coverage matrix of GAlignmentsList
coverageMatrixListFromGAL-method coverage matrix of GAlignmentsList

-- D --

defaultMapBias Generate default mapbias from genotype
defaultMapBias-method Generate default mapbias from genotype
defaultPhase defaultPhase
defaultPhase-method defaultPhase
detectAI detectAI
detectAI-method detectAI
DetectedAI DetectedAI class
DetectedAI-class DetectedAI class
DetectedAI-method DetectedAI class
DetectedAI-plot DetectedAI plot
DetectedAI-summary DetectedAI summary
DetectedAIFromArray Initialize DetectedAI
detectedAI_vs_threshold_variable_multigraph_plot DetectedAI plot
detectedAI_vs_threshold_variable_multigraph_plot-method DetectedAI plot
detectedAI_vs_threshold_variable_plot DetectedAI plot
detectedAI_vs_threshold_variable_plot-method DetectedAI plot
detectedAI_vs_threshold_variable_summary DetectedAI summary
detectedAI_vs_threshold_variable_summary-method DetectedAI summary

-- F --

fraction ASEset objects
fraction-method ASEset objects
fractionPlotDf Plot Dataframe
fractionPlotDf-method Plot Dataframe
frequency ASEset objects
frequency-method ASEset objects
frequency_vs_threshold_variable_multigraph_plot DetectedAI plot
frequency_vs_threshold_variable_multigraph_plot-method DetectedAI plot
frequency_vs_threshold_variable_plot DetectedAI plot
frequency_vs_threshold_variable_plot,DetectedAI-class DetectedAI plot
frequency_vs_threshold_variable_plot-method DetectedAI plot
frequency_vs_threshold_variable_summary DetectedAI summary
frequency_vs_threshold_variable_summary-method DetectedAI summary

-- G --

GAnalysis Initialize GlobalAnalysis
gba global analysis wrapper
gba-method global analysis wrapper
gbarplot gbarplot ASEset objects
gbarplot-method gbarplot ASEset objects
genomatrix genomatrix object
genotype ASEset objects
genotype-method ASEset objects
genotype2phase genotype2phase
genotype2phase-method genotype2phase
genotype<- ASEset objects
genotype<--method ASEset objects
getAlleleCounts snp count data
getAlleleCounts-method snp count data
getAlleleQuality snp quality data
getAlleleQuality-method snp quality data
getAnnotationDataFrame AnnotationDb wrappers
getAreaFromGeneNames Get Gene Area
getAreaFromGeneNames-method Get Gene Area
getCDSFromAnnotation AnnotationDb wrappers
getCDSVector AnnotationDb wrappers
getDefaultMapBiasExpMean Map Bias
getDefaultMapBiasExpMean-method Map Bias
getDefaultMapBiasExpMean3D Map Bias
getDefaultMapBiasExpMean3D-method Map Bias
getExonsFromAnnotation AnnotationDb wrappers
getExonsVector AnnotationDb wrappers
getGenesFromAnnotation AnnotationDb wrappers
getGenesVector AnnotationDb wrappers
getSnpIdFromLocation Get rsIDs from locations of SNP
getSnpIdFromLocation-method Get rsIDs from locations of SNP
getTranscriptsFromAnnotation AnnotationDb wrappers
getTranscriptsVector AnnotationDb wrappers
GlobalAnalysis GlobalAnalysis class
GlobalAnalysis-class GlobalAnalysis class
GlobalAnalysis-method GlobalAnalysis class
glocationplot glocationplot ASEset objects
glocationplot-method glocationplot ASEset objects
GRvariants GRvariants object

-- H --

hetFilt genotype filter methods
hetFilt-method genotype filter methods
hist histogram plots
hist-method histogram plots
histplot histogram plots

-- I --

impBamGAL Import Bam
impBamGAL-method Import Bam
impBamGRL Import Bam-2
impBamGRL.old Import Bam-2
impBcfGR Import Bcf Selection
impBcfGR-method Import Bcf Selection
impBcfGRL Import Bcf Selection
impBcfGRL-method Import Bcf Selection
implodeList.old implode list of arguments into environment
import-bam Import Bam
import-bam-2 Import Bam-2
import-bcf Import Bcf Selection
inferAlleles inference of SNPs of ASEset
inferAlleles-method inference of SNPs of ASEset
inferAltAllele inferAltAllele
inferAltAllele-method inferAltAllele
inferGenotypes infererence of genotypes from ASEset count data
inferGenotypes-method infererence of genotypes from ASEset count data
initialize-ASEset Initialize ASEset
initialize-DetectedAI Initialize DetectedAI
initialize-GlobalAnalysis Initialize GlobalAnalysis
initialize-RiskVariant Initialize RiskVariant

-- L --

legendBarplot add legend to AllelicImbalance barplot
LinkVariantAlmlof LinkVariantAlmlof class
LinkVariantAlmlof-class LinkVariantAlmlof class
LinkVariantAlmlof-method LinkVariantAlmlof class
LinkVariantAlmlof-plot plot LinkVariantAlmlof objects
locationplot locationplot ASEset objects
locationplot-method locationplot ASEset objects
lva lva
lva-method lva
lva.internal lva.internal
lva.internal-method lva.internal

-- M --

makeMaskedFasta makes masked fasta reference
makeMaskedFasta-method makes masked fasta reference
mapBias ASEset objects
mapBias-method ASEset objects
mapBias<- ASEset objects
mapBias<--method ASEset objects
mapBiasRef mapBias for reference allele
mapBiasRef-method mapBias for reference allele
maternalAllele ASEset objects
maternalAllele-method ASEset objects
minCountFilt minCountFilt methods
minCountFilt-method minCountFilt methods
minFreqFilt minFreqFilt methods
minfreqFilt minFreqFilt methods
minFreqFilt-method minFreqFilt methods
multiAllelicFilt multi-allelic filter methods
multiAllelicFilt-method multi-allelic filter methods

-- P --

paternalAllele ASEset objects
paternalAllele-method ASEset objects
phase ASEset objects
phase-method ASEset objects
phase-method RiskVariant class
phase2genotype phase2genotype
phase2genotype-method phase2genotype
phase<- ASEset objects
phase<--method ASEset objects
phase<--method RiskVariant class
phaseArray2phaseMatrix phaseArray2phaseMatrix
phaseArray2phaseMatrix-method phaseArray2phaseMatrix
phaseMatrix2Array phaseMatrix2Array
phaseMatrix2Array-method phaseMatrix2Array
plot plot LinkVariantAlmlof objects
plot-method plot LinkVariantAlmlof objects
pvalue LinkVariantAlmlof class
pvalue-method LinkVariantAlmlof class

-- R --

randomRef Random ref allele from genotype
randomRef-method Random ref allele from genotype
reads reads object
ref ASEset objects
ref-method ASEset objects
ref-method RiskVariant class
ref<- ASEset objects
ref<--method ASEset objects
ref<--method RiskVariant class
refAllele Reference allele
refAllele-method Reference allele
referenceFrequency DetectedAI class
referenceFrequency-method DetectedAI class
reference_frequency_density_vs_threshold_variable_multigraph_plot DetectedAI plot
reference_frequency_density_vs_threshold_variable_multigraph_plot-method DetectedAI plot
reference_frequency_density_vs_threshold_variable_plot DetectedAI plot
reference_frequency_density_vs_threshold_variable_plot-method DetectedAI plot
refExist ASEset objects
refExist-method ASEset objects
RegionSummary RegionSummary class
regionSummary regionSummary
RegionSummary-class RegionSummary class
RegionSummary-method RegionSummary class
regionSummary-method regionSummary
RiskVariant RiskVariant class
RiskVariant-class RiskVariant class
RiskVariant-method RiskVariant class
RiskVariantFromGRangesAndPhaseArray Initialize RiskVariant

-- S --

scanForHeterozygotes scanForHeterozygotes
scanForHeterozygotes-method scanForHeterozygotes
scanForHeterozygotes.old scanForHeterozygotes-old
sumnames RegionSummary class
sumnames-method RegionSummary class

-- T --

thresholdCountSample DetectedAI class
thresholdCountSample-method DetectedAI class
thresholdDeltaFrequency DetectedAI class
thresholdDeltaFrequency-method DetectedAI class
thresholdFrequency DetectedAI class
thresholdFrequency-method DetectedAI class
thresholdPvalue DetectedAI class
thresholdPvalue-method DetectedAI class

-- U --

usedSNPs_vs_threshold_variable_summary DetectedAI summary
usedSNPs_vs_threshold_variable_summary-method DetectedAI summary