Man pages for pappewaio/AllelicImbalance
Investigates Allele Specific Expression
| 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 |
