tadar

tadar is a package designed to enable Transcriptome Analysis of Differential Allelic Representation (DAR).

DAR is parsimoniously defined as an unequal distribution of polymorphic loci between experimental sample groups; a situation likely to be encountered in RNA-seq experiments involving organisms that lack isogenicity. When unequally-represented polymorphic loci are also expression quantitative trait loci (eQTLs), differences in gene expression between groups can be incorrectly interpreted as a consequence of the experimental condition. DAR analysis is therefore recommended as a complementary technique alongside Differential Expression analysis. DAR analysis results in an easy-to-interpret value between 0 and 1 for each feature (e.g. gene) of interest, where 0 represents identical allelic representation and 1 represents complete diversity. This metric can be used to identify features prone to false-positive calls in Differential Expression analysis, and can be leveraged with statistical methods to alleviate the impact of such artefacts on RNA-seq data.

An example of the application of DAR analysis can be found in our manuscript.

Installation

BiocManager is recommended for the installation of this package.

install.packages("BiocManager")
BiocManager::install("tadar")

The development version of this package can also be installed from GitHub.

BiocManager::install("baerlachlan/tadar")