# Transcriptome Analysis of Differential Allelic Representation

## Documentation for package ‘tadar’ version 1.9.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

assignFeatureDar | Assign DAR values to genomic features
assignFeatureDar-method | Assign DAR values to genomic features
chr1_genes | Genomic feature example data
chr1_tt | Differential expression example data
countAlleles | Count alleles within each experimental group
countAlleles-method | Count alleles within each experimental group
countsToProps | Convert allele counts to proportions
countsToProps-method | Convert allele counts to proportions
dar | Calculate Differential Allelic Representation (DAR)
dar-method | Calculate Differential Allelic Representation (DAR)
filterLoci | Filter loci
filterLoci-method | Filter loci
flipRanges | Convert DAR origin ranges to DAR region ranges, or vice versa
flipRanges-method | Convert DAR origin ranges to DAR region ranges, or vice versa
modP | DAR-moderated _p_-values
modP-method | DAR-moderated _p_-values
plotChrDar | Plot DAR across a chromosome
plotChrDar-method | Plot DAR across a chromosome
plotDarECDF | Plot the Empirical Cumulative Distribution Function of DAR
plotDarECDF-method | Plot the Empirical Cumulative Distribution Function of DAR
readGenotypes | Read genotypes from a VCF file
readGenotypes-method | Read genotypes from a VCF file
unphaseGT | Unphase genotypes
unphaseGT-method | Unphase genotypes