Investigates allele specific expression

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Documentation for package ‘AllelicImbalance’ version 1.6.2

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

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<- ASEset objects
alt<--method ASEset objects
annotation-wrappers AnnotationDb wrappers
annotationBarplot add annotation to AllelicImbalance barplot
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-gbarplot gbarplot ASEset objects
ASEset-glocationplot glocationplot ASEset objects
ASEset-gviztrack ASEset-gviztrack ASEset objects
ASEset-locationplot locationplot ASEset objects
ASEset-scanForHeterozygotes scanForHeterozygotes
ASEset.sim ASEset.sim object
ASEsetFromArrays Initialize ASEset
ASEsetFromBam ASEset from bam file
ASEsetFromBam-method ASEset from bam file
ASEsetFromCountList Initialize ASEset

-- B --

BamList snp count data
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
binom.test binomial test
binom.test-method binomial test
boxplot boxplots
boxplot-method boxplots

-- 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
DetectedAIFromArray Initialize DetectedAI

-- F --

fraction ASEset objects
fraction-method ASEset objects
fractionPlotDf Plot Dataframe
fractionPlotDf-method Plot Dataframe
frequency ASEset objects
frequency-method ASEset objects
frequency-method ReferenceBias class

-- G --

GAnalysis Initialize GlobalAnalysis
gba global analysis wrapper
gba-method global analysis wrapper
gbarplot gbarplot ASEset objects
gbarplot-method gbarplot ASEset objects
genofilters genotype filter methods
genotype ASEset objects
genotype-method ASEset objects
genotype<- ASEset objects
genotype<--method ASEset objects
getAlleleCounts snp count data
getAlleleCounts-method snp count 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
hetPerSample ReferenceBias class
hetPerSample-method ReferenceBias class
hetPerSnp ReferenceBias class
hetPerSnp-method ReferenceBias class
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-ReferenceBias Initialize ReferenceBias

-- L --

legendBarplot add legend to AllelicImbalance barplot
locationplot locationplot ASEset objects
locationplot-method locationplot ASEset objects

-- M --

makeMaskedFasta makes masked fasta reference
makeMaskedFasta-method makes masked fasta reference
mapBias ASEset objects
mapBias-method ASEset objects
mapBiasRef mapBias for reference allele
mapBiasRef-method mapBias for reference allele

-- P --

phase ASEset objects
phase-method ASEset objects
phase<- ASEset objects
phase<--method ASEset objects
phaseArray2Matrix phaseArray2Matrix
phaseArray2Matrix-method phaseArray2Matrix
phaseMatrix2Array phaseMatrix2Array
phaseMatrix2Array-method phaseMatrix2Array

-- R --

randomRef Random ref allele from genotype
randomRef-method Random ref allele from genotype
RBias Initialize ReferenceBias
reads reads object
ref ASEset objects
ref-method ASEset objects
ref<- ASEset objects
ref<--method ASEset objects
refAllele Reference allele
refAllele-method Reference allele
refbiasByAnnotation ReferenceBias class
refbiasByAnnotation-method ReferenceBias class
ReferenceBias ReferenceBias class
ReferenceBias-class ReferenceBias class
ReferenceBias-method ReferenceBias class
ReferenceBias-show genotype filter methods
ReferenceBias-show-method genotype filter methods
referenceFrequency DetectedAI class
referenceFrequency-method DetectedAI class
refFraction reference fraction
refFraction-method reference fraction
regionSummary regionSummary
regionSummary-method regionSummary

-- S --

scanForHeterozygotes scanForHeterozygotes
scanForHeterozygotes-method scanForHeterozygotes
scanForHeterozygotes.old scanForHeterozygotes-old
show-method genotype filter methods

-- 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