paularstrpo/GeTalleleR: A method for integrative analysis and visualization of DNA and RNA allele frequencies

Asymmetric allele expression typically indicates functional and/or structural features associated with the underlying genetic variants. When integrated, RNA and DNA allele frequencies can reveal patterns characteristic of a wide-range of biological traits, including ploidy changes, genome admixture, allele-specific expression and gene-dosage transcriptional response. To assess RNA and DNA allele frequencies from matched sequencing datasets, we introduce GeTallele: a mathematical model and a toolbox that provides a suit of functions for integrative analysis, statistical assessment and visualization of Genome and Transcriptome allele frequencies. The toolbox introduces a method for generating model distributions of variant allele frequencies (VAF) with a given variant read probability. Using model VAF probabilities, GeTallele allows estimation and comparison of variant read probabilities (VAF distributions) in a sequencing data sets. We demonstrate this functionality across cancer DNA and RNA sequencing data sets. Based on our evaluation, variant read probabilities can serve as a dependable indicator to assess gene and chromosomal allele asymmetries and to aid calls of genomic events in matched sequencing RNA and DNA datasets..

install.packages("remotes")
remotes::install_github("paularstrpo/GeTalleleR")