AllelicImbalance: Investigates Allele Specific Expression
Version 1.14.0

Provides a framework for allelic specific expression investigation using RNA-seq data.

AuthorJesper R Gadin, Lasse Folkersen
Bioconductor views Genetics Infrastructure Sequencing
Date of publicationNone
MaintainerJesper R Gadin <j.r.gadin@gmail.com>
LicenseGPL-3
Version1.14.0
URL https://github.com/pappewaio/AllelicImbalance
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AllelicImbalance")

Getting started

Package overview
README.md
AllelicImbalance Vignette

Popular man pages

annotation-wrappers: AnnotationDb wrappers
ASEset-barplot: barplot ASEset objects
binom.test: binomial test
countAllelesFromBam: alleleCounts from bam file
GRvariants: GRvariants object
legendBarplot: add legend to AllelicImbalance barplot
makeMaskedFasta: makes masked fasta reference
See all...

All man pages Function index File listing

Man pages

AllelicImbalance-package: A package meant to provide all basic functions for...
annotationBarplot: add annotation to AllelicImbalance barplot
annotation-wrappers: AnnotationDb wrappers
ASEset-barplot: barplot ASEset objects
ASEset-class: ASEset objects
ASEset-filters: genotype filter methods
ASEsetFromBam: ASEset from bam file
ASEset-gbarplot: gbarplot ASEset objects
ASEset-glocationplot: glocationplot ASEset objects
ASEset-gviztrack: ASEset-gviztrack ASEset objects
ASEset.old: ASEset.old object
ASEset-scanForHeterozygotes: scanForHeterozygotes
ASEset.sim: ASEset.sim object
barplot-lattice-support: lattice barplot inner functions for ASEset objects
binom.test: binomial test
chisq.test: chi-square test
cigar-utilities: realCigarPosition
countAllelesFromBam: alleleCounts from bam file
coverageMatrixListFromGAL: coverage matrix of GAlignmentsList
decorateWithExons: decorateWithExons
decorateWithGenes: decorateWithGenes
defaultMapBias: Generate default mapbias from genotype
defaultPhase: defaultPhase
detectAI: detectAI
DetectedAI-class: DetectedAI class
DetectedAI-plot: DetectedAI plot
DetectedAI-summary: DetectedAI summary
fractionPlotDf: Plot Dataframe
gba: global analysis wrapper
genomatrix: genomatrix object
genotype2phase: genotype2phase
getAlleleCounts: snp count data
getAlleleQuality: snp quality data
getAreaFromGeneNames: Get Gene Area
getDefaultMapBiasExpMean: Map Bias
getSnpIdFromLocation: Get rsIDs from locations of SNP
GlobalAnalysis-class: GlobalAnalysis class
GRvariants: GRvariants object
histplot: histogram plots
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
inferAltAllele: inferAltAllele
inferGenotypes: infererence of genotypes from ASEset count data
initialize-ASEset: Initialize ASEset
initialize-DetectedAI: Initialize DetectedAI
initialize-GlobalAnalysis: Initialize GlobalAnalysis
initialize-RiskVariant: Initialize RiskVariant
legendBarplot: add legend to AllelicImbalance barplot
LinkVariantAlmlof-class: LinkVariantAlmlof class
LinkVariantAlmlof-plot: plot LinkVariantAlmlof objects
locationplot: locationplot ASEset objects
lva: lva
lva.internal: lva.internal
makeMaskedFasta: makes masked fasta reference
mapBiasRef: mapBias for reference allele
minCountFilt: minCountFilt methods
minFreqFilt: minFreqFilt methods
multiAllelicFilt: multi-allelic filter methods
phase2genotype: phase2genotype
phaseArray2phaseMatrix: phaseArray2phaseMatrix
phaseMatrix2Array: phaseMatrix2Array
randomRef: Random ref allele from genotype
reads: reads object
refAllele: Reference allele
regionSummary: regionSummary
RegionSummary-class: RegionSummary class
RiskVariant-class: RiskVariant class
scanForHeterozygotes-old: scanForHeterozygotes-old

Functions

ASEDAnnotationTrack Man page Man page
ASEDAnnotationTrack,ASEset-method Man page 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 Man page
ASEsetFromBam,GRanges-method Man page Man page
ASEsetFromCountList Man page Man page Source code
AllelicImbalance Man page
AllelicImbalance-package Man page
CoverageDataTrack Man page Man page
CoverageDataTrack,ASEset-method Man page
DetectedAI Man page
DetectedAI-class Man page 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 Man page
GlobalAnalysis-method Man page
IRangesFromIntegerList Source code
LinkVariantAlmlof Man page
LinkVariantAlmlof-class Man page Man page
LinkVariantAlmlof-method Man page
LinkVariantAlmlof-plot Man page
Na2False Source code
RegionSummary Man page
RegionSummary-class Man page Man page
RegionSummary-method Man page
RiskVariant Man page
RiskVariant-class Man page Man page
RiskVariant-method Man page
RiskVariantFromGRangesAndPhaseArray Man page Source code
addLva2ASEset Source code
aiRegionDirectionFromMaternalPhaseMapBiasAndIndex Source code
alleleCounts Man page Man page
alleleCounts,ASEset-method Man page Man page
alleleCounts<- Man page Man page
alleleCounts<-,ASEset-method Man page 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 Man page
arank,ASEset-method Man page
array2MatrixList Source code
arrayFromAlleleVector Source code
barplot Man page Man page
barplot,ASEset-method Man page Man page
barplot-lattice-support Man page
barplotLatticeCounts Man page Man page Source code
barplotLatticeFraction Man page Man page Source code Source code
basic Man page
basic,RegionSummary-method Man page
binom.test Man page
binom.test,ASEset-method Man page Man page
calcFrequencyFromAlleleCounts Source code
chisq.test Man page
chisq.test,ASEset-method Man page Man page
cigar-utilities Man page
countAllelesFromBam Man page Man page
countAllelesFromBam,GRanges-method Man page Man page
countsPerSample Man page
countsPerSample,ASEset-method Man page
countsPerSnp Man page
countsPerSnp,ASEset-method Man page
coverageMatrixListFromGAL Man page Man page
coverageMatrixListFromGAL,GAlignmentsList-method Man page Man page
decorateWithExons Man page Source code
decorateWithGenes Man page Source code
defaultMapBias Man page Man page
defaultMapBias,ASEset-method Man page Man page
defaultPhase Man page Man page
defaultPhase,numeric-method Man page Man page
deltaFromFractionMatrixAndMapBias Source code
detectAI Man page
detectAI,ASEset-method Man page 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 Man page
detectedAI_vs_threshold_variable_summary,DetectedAI-method Man page Man page
expandMatrixToArray Source code
fraction Man page Man page
fraction,ASEset-method Man page Man page
fractionPlotDf Man page Man page
fractionPlotDf,ASEset-method Man page Man page
frequency Man page 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 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 Man page
frequency_vs_threshold_variable_summary,DetectedAI-method Man page Man page
gba Man page Man page
gba,character-method Man page Man page
gbarplot Man page
gbarplot,ASEset-method Man page
genomatrix Man page
genotype Man page Man page
genotype,ASEset-method Man page Man page
genotype2phase Man page Man page
genotype2phase,matrix-method Man page Man page
genotype<- Man page Man page
genotype<-,ASEset-method Man page Man page
genotypeArray2genotypeMatrix Source code
getAlleleCount Source code
getAlleleCounts Man page Man page
getAlleleCounts,GAlignmentsList-method Man page Man page
getAlleleQuality Man page Man page
getAlleleQuality,GAlignmentsList-method Man page Man page
getAnnotationDataFrame Man page Man page Source code
getAreaFromGeneNames Man page Man page
getAreaFromGeneNames,character-method Man page Man page
getCDSFromAnnotation Man page Man page Source code
getCDSVector Man page Man page Source code
getDefaultMapBiasExpMean Man page Man page
getDefaultMapBiasExpMean,ANY-method Man page
getDefaultMapBiasExpMean,list-method Man page
getDefaultMapBiasExpMean3D Man page Man page
getDefaultMapBiasExpMean3D,ANY-method Man page Man page
getExonsFromAnnotation Man page Man page Source code
getExonsVector Man page Man page Source code
getGenesFromAnnotation Man page Man page Source code
getGenesVector Man page Man page Source code
getSnpIdFromLocation Man page Man page
getSnpIdFromLocation,GRanges-method Man page Man page
getTranscriptsFromAnnotation Man page Man page Source code
getTranscriptsVector Man page Man page Source code
glocationplot Man page
glocationplot,ASEset-method Man page
groupBasedOnPhaseAndAlleleCombination Source code
hetFilt Man page Man page
hetFilt,ASEset-method Man page Man page
heterozygozityFromPhaseArray Source code
hist Man page
hist,ASEset-method Man page
hist,ReferenceBias-method Man page
histplot Man page
impBamGAL Man page Man page
impBamGAL,character-method Man page Man page
impBamGRL Man page Source code
impBamGRL.old Man page Source code
impBcfGR Man page Man page
impBcfGR,character-method Man page Man page
impBcfGRL Man page Man page
impBcfGRL,character-method Man page 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
list.depth Source code
locationplot Man page
locationplot,ASEset-method Man page Man page
lva Man page Man page
lva,ASEset-method Man page
lva,array-method Man page
lva.internal Man page Man page
lva.internal,array-method Man page Man page
lvaGroups Source code
lvaRegressionPvalue Source code
lvaRegressionReturnCommonParamMatrix Source code
lvaRegressionReturnCommonParamMatrix.nlme Source code
lvaRegressionReturnCommonParamMatrixTxSNPspecific Source code
lvaRegressionReturnCommonParamMatrixTxSNPspecific.nlme Source code
makeMaskedFasta Man page Man page
makeMaskedFasta,character-method Man page Man page
makeMetaASEsetDataFrameForRegionSummary Source code
makeRegionGRangesFromASEsetWithRegionIndex Source code
mapBias Man page Man page
mapBias,ASEset-method Man page Man page
mapBias<- Man page
mapBias<-,ASEset-method Man page
mapBiasRef Man page Man page
mapBiasRef,ASEset-method Man page Man page
maternalAllele Man page
maternalAllele,ASEset-method Man page
maternalPhaseMapBias Source code
matrixFromLmListCommonParam Source code
mergeDirAndFilename Source code
mergePhaseArray2phaseMatrix Source code
minCountFilt Man page Man page
minCountFilt,ASEset-method Man page Man page
minFreqFilt Man page Man page
minFreqFilt,ASEset-method Man page Man page
minfreqFilt Man page
minusStrandCountsExists Source code
multiAllelicFilt Man page Man page
multiAllelicFilt,ASEset-method Man page Man page
multiUnlist Source code
multiUnlist.index Source code
multiUnlist.index.names Source code
paternalAllele Man page
paternalAllele,ASEset-method Man page
phase Man page Man page
phase,ASEset-method Man page Man page
phase,RiskVariant-method Man page
phase2genotype Man page Man page
phase2genotype,array-method Man page Man page
phase<- Man page Man page
phase<-,ASEset-method Man page Man page
phase<-,RiskVariant-method Man page
phaseArray2genotypeArray Source code
phaseArray2phaseMatrix Man page Man page
phaseArray2phaseMatrix,array-method Man page Man page
phaseMatrix2Array Man page Man page
phaseMatrix2Array,matrix-method Man page Man page
pickSecondMostExpressedAllele Source code
plot Man page Man page
plot,LinkVariantAlmlof,ANY-method Man page
plot,LinkVariantAlmlof-method Man page
plusStrandCountsExists Source code
pvalue Man page
pvalue,LinkVariantAlmlof-method Man page
randomRef Man page Man page
randomRef,ASEset-method Man page 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 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
region.list.populate Source code
regionStatisticsFromMatrixAndIndex Source code
regionSummary Man page Man page
regionSummary,ASEset-method Man page
regionSummary,numeric-method Man page
returnMaternalPhaseFrequency Source code
scanForHeterozygotes Man page Man page
scanForHeterozygotes,ASEset-method Man page
scanForHeterozygotes,GAlignmentsList-method Man page
scanForHeterozygotes.old Man page Source code
selectRegionAndTransferIndexToASEset Source code
splitGenotypeCount Source code
splitGenotypeMatrix Source code
splitGenotypePickAltAllele Source code
splitGenotypePickRefAllele Source code
splitGenotypeRank Source code
subsetArrayToMatrix 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
toKeepMatrixMinCountFilterAll Source code
toKeepMatrixMinCountFilterEach Source code
toKeepMatrixMinFreqFilterAll Source code
toKeepMatrixMinFreqFilterEach Source code
unknownStrandCountsExists Source code
unlistGRangesListAndIndex Source code
usedSNPs_vs_threshold_variable_summary Man page
usedSNPs_vs_threshold_variable_summary,DetectedAI-method Man page
verboseCoerceToCharacter Source code

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/ASEset-class.R
R/AllelicImbalance-package.R
R/DetectedAI-class.R
R/GlobalAnalysis-class.R
R/GvizTrack-methods.R
R/LinkVariantAlmlof-class.R
R/RegionSummary-class.R
R/RiskVariant-class.R
R/auxillary-functions-annotation.R
R/auxillary-functions-visuals.R
R/auxillary-methods-annotation.R
R/auxillary-methods-summaries.R
R/auxillary-methods.R
R/barplot-methods.R
R/binom.test-methods.R
R/boxplot-methods.R
R/chisq.test-methods.R
R/deprecations.R
R/detect-methods.R
R/filter-methods.R
R/histplot-methods.R
R/inference-methods.R
R/initialize-methods.R
R/linkage-methods.R
R/list-methods.R
R/locationplot-methods.R
R/mapbias-methods.R
R/plot-methods.R
R/show-methods.R
R/simulation-methods.R
R/summary-methods.R
R/utils.R
README.md
build
build/vignette.rds
data
data/ASEset.rdata
data/ASEset.sim.rdata
data/GRvariants.rdata
data/genomatrix.rdata
data/reads.rdata
inst
inst/CITATION
inst/doc
inst/doc/AllelicImbalance-vignette.R
inst/doc/AllelicImbalance-vignette.Rmd
inst/doc/AllelicImbalance-vignette.pdf
inst/extdata
inst/extdata/ERP000101_subset
inst/extdata/ERP000101_subset/ERP000101.bcf
inst/extdata/ERP000101_subset/ERP000101.bcf.bci
inst/extdata/ERP000101_subset/ERP000101.vcf
inst/extdata/ERP000101_subset/ERR009097.bam
inst/extdata/ERP000101_subset/ERR009097.bam.bai
inst/extdata/ERP000101_subset/ERR009102.bam
inst/extdata/ERP000101_subset/ERR009102.bam.bai
inst/extdata/ERP000101_subset/ERR009103.bam
inst/extdata/ERP000101_subset/ERR009103.bam.bai
inst/extdata/ERP000101_subset/ERR009113.bam
inst/extdata/ERP000101_subset/ERR009113.bam.bai
inst/extdata/ERP000101_subset/ERR009115.bam
inst/extdata/ERP000101_subset/ERR009115.bam.bai
inst/extdata/ERP000101_subset/ERR009122.bam
inst/extdata/ERP000101_subset/ERR009122.bam.bai
inst/extdata/ERP000101_subset/ERR009126.bam
inst/extdata/ERP000101_subset/ERR009126.bam.bai
inst/extdata/ERP000101_subset/ERR009127.bam
inst/extdata/ERP000101_subset/ERR009127.bam.bai
inst/extdata/ERP000101_subset/ERR009129.bam
inst/extdata/ERP000101_subset/ERR009129.bam.bai
inst/extdata/ERP000101_subset/ERR009135.bam
inst/extdata/ERP000101_subset/ERR009135.bam.bai
inst/extdata/ERP000101_subset/ERR009141.bam
inst/extdata/ERP000101_subset/ERR009141.bam.bai
inst/extdata/ERP000101_subset/ERR009142.bam
inst/extdata/ERP000101_subset/ERR009142.bam.bai
inst/extdata/ERP000101_subset/ERR009144.bam
inst/extdata/ERP000101_subset/ERR009144.bam.bai
inst/extdata/ERP000101_subset/ERR009146.bam
inst/extdata/ERP000101_subset/ERR009146.bam.bai
inst/extdata/ERP000101_subset/ERR009147.bam
inst/extdata/ERP000101_subset/ERR009147.bam.bai
inst/extdata/ERP000101_subset/ERR009154.bam
inst/extdata/ERP000101_subset/ERR009154.bam.bai
inst/extdata/ERP000101_subset/ERR009157.bam
inst/extdata/ERP000101_subset/ERR009157.bam.bai
inst/extdata/ERP000101_subset/ERR009159.bam
inst/extdata/ERP000101_subset/ERR009159.bam.bai
inst/extdata/ERP000101_subset/ERR009160.bam
inst/extdata/ERP000101_subset/ERR009160.bam.bai
inst/extdata/ERP000101_subset/ERR009167.bam
inst/extdata/ERP000101_subset/ERR009167.bam.bai
inst/extdata/hg19.chr17.subset.fa
inst/extdata/hg19.chr17.subset.fa.fai
inst/unitTests
man
man/ASEset-barplot.Rd
man/ASEset-class.Rd
man/ASEset-filters.Rd
man/ASEset-gbarplot.Rd
man/ASEset-glocationplot.Rd
man/ASEset-gviztrack.Rd
man/ASEset-scanForHeterozygotes.Rd
man/ASEset.old.Rd
man/ASEset.sim.Rd
man/ASEsetFromBam.Rd
man/AllelicImbalance-package.Rd
man/DetectedAI-class.Rd
man/DetectedAI-plot.Rd
man/DetectedAI-summary.Rd
man/GRvariants.Rd
man/GlobalAnalysis-class.Rd
man/LinkVariantAlmlof-class.Rd
man/LinkVariantAlmlof-plot.Rd
man/RegionSummary-class.Rd
man/RiskVariant-class.Rd
man/annotation-wrappers.Rd
man/annotationBarplot.Rd
man/barplot-lattice-support.Rd
man/binom.test.Rd
man/chisq.test.Rd
man/cigar-utilities.Rd
man/countAllelesFromBam.Rd
man/coverageMatrixListFromGAL.Rd
man/decorateWithExons.Rd
man/decorateWithGenes.Rd
man/defaultMapBias.Rd
man/defaultPhase.Rd
man/detectAI.Rd
man/fractionPlotDf.Rd
man/gba.Rd
man/genomatrix.Rd
man/genotype2phase.Rd
man/getAlleleCounts.Rd
man/getAlleleQuality.Rd
man/getAreaFromGeneNames.Rd
man/getDefaultMapBiasExpMean.Rd
man/getSnpIdFromLocation.Rd
man/histplot.Rd
man/implodeList-old.Rd
man/import-bam-2.Rd
man/import-bam.Rd
man/import-bcf.Rd
man/inferAlleles.Rd
man/inferAltAllele.Rd
man/inferGenotypes.Rd
man/initialize-ASEset.Rd
man/initialize-DetectedAI.Rd
man/initialize-GlobalAnalysis.Rd
man/initialize-RiskVariant.Rd
man/legendBarplot.Rd
man/locationplot.Rd
man/lva.Rd
man/lva.internal.Rd
man/makeMaskedFasta.Rd
man/mapBiasRef.Rd
man/minCountFilt.Rd
man/minFreqFilt.Rd
man/multiAllelicFilt.Rd
man/phase2genotype.Rd
man/phaseArray2phaseMatrix.Rd
man/phaseMatrix2Array.Rd
man/randomRef.Rd
man/reads.Rd
man/refAllele.Rd
man/regionSummary.Rd
man/scanForHeterozygotes-old.Rd
tests
tests/test-all.R
tests/testthat
tests/testthat/test_calc_arank.R
tests/testthat/test_calc_frequency.R
tests/testthat/test_cigar_utility.R
tests/testthat/test_detectAI.R
tests/testthat/test_filters.R
tests/testthat/test_fraction.R
tests/testthat/test_frequency.R
tests/testthat/test_genotype2phase.R
tests/testthat/test_import_counts.R
tests/testthat/test_infer_alleles.R
tests/testthat/test_infer_genotypes.R
tests/testthat/test_lva.R
tests/testthat/test_phase.R
tests/testthat/test_phase2genotype.R
tests/testthat/test_phaseArray2phaseMatrix.R
tests/testthat/test_refFraction.R
tests/testthat/test_regionSummary.R
tests/testthat/test_utils.R
vignettes
vignettes/AllelicImbalance-vignette.Rmd
AllelicImbalance documentation built on May 20, 2017, 10:13 p.m.

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