AllelicImbalance: Investigates Allele Specific Expression

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

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("AllelicImbalance")
AuthorJesper R Gadin, Lasse Folkersen
Bioconductor views Genetics Infrastructure Sequencing
Date of publicationNone
MaintainerJesper R Gadin <j.r.gadin@gmail.com>
LicenseGPL-3
Version1.12.0
https://github.com/pappewaio/AllelicImbalance

View on Bioconductor

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

alleleCounts Man page
alleleCounts<- Man page
alleleCounts<-,ASEset-method Man page
alleleCounts,ASEset-method Man page
AllelicImbalance Man page
AllelicImbalance-package Man page
alt Man page
alt<- Man page
alt<-,ASEset,ANY-method Man page
alt,ASEset-method Man page
altExist Man page
altExist,ASEset-method Man page
alt<-,RiskVariant,ANY-method Man page
alt,RiskVariant-method Man page
annotationBarplot Man page
annotation-wrappers Man page
aquals Man page
aquals<- Man page
aquals<-,ASEset-method Man page
aquals,ASEset-method Man page
arank Man page
arank,ASEset-method Man page
ASEDAnnotationTrack Man page
ASEDAnnotationTrack,ASEset-method Man page
ASEset Man page
ASEset-barplot Man page
ASEset-class Man page
ASEset-filters Man page
ASEsetFromArrays Man page
ASEsetFromBam Man page
ASEsetFromBam,GRanges-method Man page
ASEsetFromCountList Man page
ASEset-gbarplot Man page
ASEset-glocationplot Man page
ASEset-gviztrack Man page
ASEset-locationplot Man page
ASEset.old Man page
ASEset-scanForHeterozygotes Man page
ASEset.sim Man page
barplot Man page
barplot,ASEset-method Man page
barplotLatticeCounts Man page
barplotLatticeFraction Man page
barplot-lattice-support Man page
basic Man page
basic,RegionSummary-method Man page
binom.test Man page
binom.test,ASEset-method Man page
chisq.test Man page
chisq.test,ASEset-method Man page
cigar-utilities Man page
countAllelesFromBam Man page
countAllelesFromBam,GRanges-method Man page
countsPerSample Man page
countsPerSample,ASEset-method Man page
countsPerSnp Man page
countsPerSnp,ASEset-method Man page
CoverageDataTrack Man page
CoverageDataTrack,ASEset-method Man page
coverageMatrixListFromGAL Man page
coverageMatrixListFromGAL,GAlignmentsList-method Man page
decorateWithExons Man page
decorateWithGenes Man page
defaultMapBias Man page
defaultMapBias,ASEset-method Man page
defaultPhase Man page
defaultPhase,numeric-method Man page
detectAI Man page
detectAI,ASEset-method Man page
DetectedAI Man page
DetectedAI-class Man page
DetectedAIFromArray Man page
DetectedAI-method Man page
DetectedAI-plot Man page
DetectedAI-summary 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
detectedAI_vs_threshold_variable_summary,DetectedAI-method Man page
fraction Man page
fraction,ASEset-method Man page
fractionPlotDf Man page
fractionPlotDf,ASEset-method Man page
frequency 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
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
frequency_vs_threshold_variable_summary,DetectedAI-method Man page
GAnalysis Man page
gba Man page
gba,character-method Man page
gbarplot Man page
gbarplot,ASEset-method Man page
genomatrix Man page
genotype Man page
genotype<- Man page
genotype2phase Man page
genotype2phase,matrix-method Man page
genotype<-,ASEset-method Man page
genotype,ASEset-method Man page
getAlleleCounts Man page
getAlleleCounts,GAlignmentsList-method Man page
getAlleleQuality Man page
getAlleleQuality,GAlignmentsList-method Man page
getAnnotationDataFrame Man page
getAreaFromGeneNames Man page
getAreaFromGeneNames,character-method Man page
getCDSFromAnnotation Man page
getCDSVector Man page
getDefaultMapBiasExpMean Man page
getDefaultMapBiasExpMean3D Man page
getDefaultMapBiasExpMean3D,ANY-method Man page
getDefaultMapBiasExpMean,ANY-method Man page
getDefaultMapBiasExpMean,list-method Man page
getExonsFromAnnotation Man page
getExonsVector Man page
getGenesFromAnnotation Man page
getGenesVector Man page
getSnpIdFromLocation Man page
getSnpIdFromLocation,GRanges-method Man page
getTranscriptsFromAnnotation Man page
getTranscriptsVector Man page
GlobalAnalysis Man page
GlobalAnalysis-class Man page
GlobalAnalysis-method Man page
glocationplot Man page
glocationplot,ASEset-method Man page
GRvariants Man page
hetFilt Man page
hetFilt,ASEset-method Man page
hist Man page
hist,ASEset-method Man page
histplot Man page
hist,ReferenceBias-method Man page
impBamGAL Man page
impBamGAL,character-method Man page
impBamGRL Man page
impBamGRL.old Man page
impBcfGR Man page
impBcfGR,character-method Man page
impBcfGRL Man page
impBcfGRL,character-method Man page
implodeList.old Man page
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
LinkVariantAlmlof Man page
LinkVariantAlmlof-class Man page
LinkVariantAlmlof-method Man page
LinkVariantAlmlof-plot Man page
locationplot Man page
locationplot,ASEset-method Man page
lva Man page
lva,array-method Man page
lva,ASEset-method Man page
lva.internal Man page
lva.internal,array-method Man page
makeMaskedFasta Man page
makeMaskedFasta,character-method Man page
mapBias Man page
mapBias<- Man page
mapBias<-,ASEset-method Man page
mapBias,ASEset-method Man page
mapBiasRef Man page
mapBiasRef,ASEset-method Man page
maternalAllele Man page
maternalAllele,ASEset-method Man page
minCountFilt Man page
minCountFilt,ASEset-method Man page
minfreqFilt Man page
minFreqFilt Man page
minFreqFilt,ASEset-method Man page
multiAllelicFilt Man page
multiAllelicFilt,ASEset-method Man page
paternalAllele Man page
paternalAllele,ASEset-method Man page
phase Man page
phase<- Man page
phase2genotype Man page
phase2genotype,array-method Man page
phaseArray2phaseMatrix Man page
phaseArray2phaseMatrix,array-method Man page
phase<-,ASEset-method Man page
phase,ASEset-method Man page
phaseMatrix2Array Man page
phaseMatrix2Array,matrix-method Man page
phase<-,RiskVariant-method Man page
phase,RiskVariant-method Man page
plot Man page
plot,LinkVariantAlmlof,ANY-method Man page
plot,LinkVariantAlmlof-method Man page
pvalue Man page
pvalue,LinkVariantAlmlof-method Man page
randomRef Man page
randomRef,ASEset-method Man page
reads Man page
realCigarPosition Man page
realCigarPosition.old Man page
realCigarPositions Man page
realCigarPositionsList Man page
realCigarPositionsList.old Man page
realCigarPositions.old Man page
ref Man page
ref<- Man page
refAllele Man page
refAllele,ASEset-method Man page
ref<-,ASEset,ANY-method Man page
ref,ASEset-method Man page
referenceFrequency Man page
reference_frequency_density_vs_threshold_variable_multigraph_plo Man page
reference_frequency_density_vs_threshold_variable_plot Man page
reference_frequency_density_vs_threshold_variable_plot,DetectedA Man page
referenceFrequency,DetectedAI-method Man page
refExist Man page
refExist,ASEset-method Man page
ref<-,RiskVariant,ANY-method Man page
ref,RiskVariant-method Man page
regionSummary Man page
RegionSummary Man page
regionSummary,ASEset-method Man page
RegionSummary-class Man page
RegionSummary-method Man page
regionSummary,numeric-method Man page
RiskVariant Man page
RiskVariant-class Man page
RiskVariantFromGRangesAndPhaseArray Man page
RiskVariant-method Man page
scanForHeterozygotes Man page
scanForHeterozygotes,ASEset-method Man page
scanForHeterozygotes,GAlignmentsList-method Man page
scanForHeterozygotes.old Man page
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
usedSNPs_vs_threshold_variable_summary Man page
usedSNPs_vs_threshold_variable_summary,DetectedAI-method Man page

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

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