AllelicImbalance: Investigates Allele Specific Expression

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

Author
Jesper R Gadin, Lasse Folkersen
Date of publication
None
Maintainer
Jesper R Gadin <j.r.gadin@gmail.com>
License
GPL-3
Version
1.12.0
URLs

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

Files in this package

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