# Investigates Allele Specific Expression

## Documentation for package ‘AllelicImbalance’ version 1.16.0

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

## Help Pages

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