rmskStats
Overview
This is a standard R package providing tools to perform hit counts and enrichment/depletion analysis for repeat elements annotated by Repeat Master track (RMSK). The user must be familiar with class types and sequence analysis tools supported by Bioconductor such as the SummerizedExperiment object and DESeq2 package.
The hit counts for repeat elements (repName) is similiar to the summarizeOverlaps() function from the GenomicAlignments with extra adjustment w.r.t. numbers of reported multiple alignment (NH column). DESeq2 is used to identify the up/down-regulated repeat elements (repName). The enrichment/depletion analysis uses Hypergeometric test to determ the significance of the enrichment state of a repeat family (repFamily) or class (repClass).
This package is under development and will soon be submitted to Bioconductor repository.