AllelicImbalance-package | A package meant to provide all basic functions for high-throughput allele specific expression analysis |
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<- | ASEset objects |
alt<--method | ASEset objects |
annotation-wrappers | AnnotationDb wrappers |
annotationBarplot | add annotation to AllelicImbalance barplot |
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-gbarplot | gbarplot ASEset objects |
ASEset-glocationplot | glocationplot ASEset objects |
ASEset-gviztrack | ASEset-gviztrack ASEset objects |
ASEset-locationplot | locationplot ASEset objects |
ASEset-scanForHeterozygotes | scanForHeterozygotes |
ASEset.sim | ASEset.sim object |
ASEsetFromArrays | Initialize ASEset |
ASEsetFromBam | ASEset from bam file |
ASEsetFromBam-method | ASEset from bam file |
ASEsetFromCountList | Initialize ASEset |
BamList | snp count data |
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 |
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 |
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 |
DetectedAIFromArray | Initialize DetectedAI |
fraction | ASEset objects |
fraction-method | ASEset objects |
fractionPlotDf | Plot Dataframe |
fractionPlotDf-method | Plot Dataframe |
frequency | ASEset objects |
frequency-method | ASEset objects |
frequency-method | ReferenceBias class |
GAnalysis | Initialize GlobalAnalysis |
gba | global analysis wrapper |
gba-method | global analysis wrapper |
gbarplot | gbarplot ASEset objects |
gbarplot-method | gbarplot ASEset objects |
genofilters | genotype filter methods |
genotype | ASEset objects |
genotype-method | ASEset objects |
genotype<- | ASEset objects |
genotype<--method | ASEset objects |
getAlleleCounts | snp count data |
getAlleleCounts-method | snp count 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 |
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 |
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-ReferenceBias | Initialize ReferenceBias |
legendBarplot | add legend to AllelicImbalance barplot |
locationplot | locationplot ASEset objects |
locationplot-method | locationplot ASEset objects |
makeMaskedFasta | makes masked fasta reference |
makeMaskedFasta-method | makes masked fasta reference |
mapBias | ASEset objects |
mapBias-method | ASEset objects |
mapBiasRef | mapBias for reference allele |
mapBiasRef-method | mapBias for reference allele |
phase | ASEset objects |
phase-method | ASEset objects |
phase<- | ASEset objects |
phase<--method | ASEset objects |
phaseArray2Matrix | phaseArray2Matrix |
phaseArray2Matrix-method | phaseArray2Matrix |
phaseMatrix2Array | phaseMatrix2Array |
phaseMatrix2Array-method | phaseMatrix2Array |
randomRef | Random ref allele from genotype |
randomRef-method | Random ref allele from genotype |
RBias | Initialize ReferenceBias |
reads | reads object |
ref | ASEset objects |
ref-method | ASEset objects |
ref<- | ASEset objects |
ref<--method | ASEset objects |
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 |
referenceFrequency | DetectedAI class |
referenceFrequency-method | DetectedAI class |
refFraction | reference fraction |
refFraction-method | reference fraction |
regionSummary | regionSummary |
regionSummary-method | regionSummary |
scanForHeterozygotes | scanForHeterozygotes |
scanForHeterozygotes-method | scanForHeterozygotes |
scanForHeterozygotes.old | scanForHeterozygotes-old |
show-method | genotype filter methods |
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 |