Investigates allele specific expression


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Documentation for package ‘AllelicImbalance’ version 1.4.2

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

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
annotation-wrappers AnnotationDb wrappers
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-glocationplot glocationplot ASEset objects
ASEset-gviztrack ASEset-gviztrack ASEset objects
ASEset-lbarplot lbarplot ASEset objects
ASEset-locationplot locationplot ASEset objects
ASEset.sim ASEset.sim object
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
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
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

-- D --

defaultMapBias Generate default mapbias from genotype
defaultMapBias-method Generate default mapbias from genotype
detectAI detectAI
detectAI-method detectAI

-- F --

fraction ASEset objects
fraction-method ASEset objects
frequency ASEset objects
frequency-method ASEset objects
frequency-method ReferenceBias class

-- G --

genofilters genotype filter methods
genotype ASEset objects
genotype-method ASEset objects
genotype<- ASEset objects
genotype<--method ASEset objects
getAlleleCounts snp count data
getAnnotationDataFrame AnnotationDb wrappers
getAreaFromGeneNames Get Gene Area
getCDSFromAnnotation AnnotationDb wrappers
getCDSVector AnnotationDb wrappers
getDefaultMapBiasExpMean Map Bias
getDefaultMapBiasExpMean3D Map Bias
getExonsFromAnnotation AnnotationDb wrappers
getExonsVector AnnotationDb wrappers
getGenesFromAnnotation AnnotationDb wrappers
getGenesVector AnnotationDb wrappers
getSnpIdFromLocation Get rsIDs from locations of SNP
getTranscriptsFromAnnotation AnnotationDb wrappers
getTranscriptsVector AnnotationDb wrappers
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
impBamGRL Import Bam
impBcfGR Import Bcf Selection
impBcfGRL Import Bcf Selection
implodeList implode list of arguments into environment
import-bam Import Bam
import-bcf Import Bcf Selection
inferAlleles inference of SNPs of ASEset
inferAlleles-method inference of SNPs of ASEset
inferGenotypes infererence of genotypes from ASEset count data
inferGenotypes-method infererence of genotypes from ASEset count data
initialize-ASEset Initialize ASEset
initialize-ReferenceBias Initialize ReferenceBias

-- L --

lbarplot lbarplot ASEset objects
lbarplot-method lbarplot ASEset objects
locationplot locationplot ASEset objects
locationplot-method locationplot ASEset objects

-- M --

mapBias ASEset objects
mapBias-method ASEset objects

-- R --

RBias Initialize ReferenceBias
reads reads object
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
refFraction reference fraction
refFraction-method reference fraction

-- S --

scanForHeterozygotes scanForHeterozygotes
show-method genotype filter methods