tfboot: Bootstrapping and statistical analysis for transcription factor binding site-disrupting variants in gene sets

Abstract

MotivationGenetic variants in noncoding regions can drive changes in phenotype disrupting transcription factor binding site (TFBS) motifs. Other tools including motifbreakR have been developed to assess the impact of TFBS-disrupting variants. Here we introduce the tfboot package for statistically evaluating the TFBS disruption across a set of variants in upstream promoter regions. ResultsThe tfboot package builds on motifbreakR, plyranges, and GenomicRanges to provide methods for bootstrapping TFBS disruption to statistically quantify the impact across gene sets of interest compared to an empirical null distribution. We demonstrate the analysis here on variants in the elephant genome. The tfboot package readily integrates with Bioconductor and tidyverse-based workflows. AvailabilityThe tfboot package is implemented as an R package and is released under the MIT license at https://github.com/colossal-compsci/tfboot.