Investigates Allele Specific Expression

Documentation for package ‘AllelicImbalance’ version 1.40.0

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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