motifbreakR

Documentation

See the motifbreakR vignette on Bioconductor, or vignette("motifbreakR-vignette", package = "motifbreakR"), for an introduction to motifbreakR

See help("motifbreakR") for detailed help with running motifbreakR.

See help("plotMB") for detailed help with visualization.

Please cite:

Coetzee SG, Hazelett DJ (2024). motifbreakR v2: expanded variant analysis including indels and integrated evidence from transcription factor binding databases. Bioinformatics Advances, 4(1), vbae162. doi:10.1093/bioadv/vbae162
Coetzee SG, Coetzee GA, Hazelett DJ (2015). motifbreakR: an R/Bioconductor package for predicting variant effects at transcription factor binding sites. Bioinformatics, 31(23), 3847-3849. doi:10.1093/bioinformatics/btv470

Abstract

Functional annotation represents a key step toward the understanding and interpretation of germline and somatic variation as revealed by genome wide association studies (GWAS) and The Cancer Genome Atlas (TCGA), respectively. GWAS have revealed numerous genetic risk variants residing in non-coding DNA associated with complex diseases. For sequences that lie within enhancers or promoters of transcription, it is straightforward to assess the effects of variants on likely transcription factor binding sites. We introduce motifbreakR, which allows the biologist to judge whether the sequence surrounding a polymorphism or mutation (a single nucleotide variant or a small insertion or deletion) is a good match, and how much information is gained or lost in one allele of the polymorphism relative to another or mutation vs. wildtype. MotifbreakR is flexible, giving a choice of algorithms for interrogation of genomes with motifs from public sources that users can choose from; these are 1) a weighted-sum, 2) log-probabilities, and 3) relative entropy. MotifbreakR can predict effects for novel or previously described variants in public databases, making it suitable for tasks beyond the scope of its original design. Lastly, it can be used to interrogate any genome curated within Bioconductor.

Install

motifbreakR is available from Bioconductor:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("motifbreakR")

The examples and vignette also use genome and SNP annotation packages, for example:

BiocManager::install(c("BSgenome.Hsapiens.UCSC.hg19",
                       "SNPlocs.Hsapiens.dbSNP155.GRCh37"))

Development version

The development version can be installed from GitHub:

BiocManager::install("Simon-Coetzee/motifBreakR")