calculatePvalue         Calculate the significance of the matches for
                        the reference and alternate alleles for the for
                        their PWM
encodemotif             MotifDb object containing motif information
                        from the known and discovered motifs for the
                        ENCODE TF ChIP-seq datasets.
example.results         Example Results from motifbreakR
factorbook              MotifDb object containing motif information
                        from around the genomic regions bound by 119
                        human transcription factors in Factorbook.
hocomoco                MotifDb object containing motif information
                        from Homo Sapiens Comprehensive Model
                        Collection (HOCOMOCO) of transcription factor
                        (TF) binding models
homer                   MotifDb object containing motif information
                        from motif databases included in HOMER.
motifbreakR             Predict The Disruptiveness Of Single Nucleotide
                        Polymorphisms On Transcription Factor Binding
                        Sites.
motifbreakR_motif       MotifDb object containing motif information
                        from the motif databases of HOCOMOCO, Homer,
                        FactorBook and ENCODE
plotMB                  Plot a genomic region surrounding a genomic
                        variant, and potentially disrupted motifs
scoreAllWindows         scoreMotif.a <- function(snp.seq, ppm, len,
                        offset = 1) snp.seq <- snp.seq[offset:(offset +
                        len - 1)] ## diag code position.probs <-
                        c(ppm[snp.seq, ])[1L + 0L:(len - 1L) * (len +
                        1L)] return(position.probs) #' @importFrom
                        compiler cmpfun scoreMotif <-
                        cmpfun(scoreMotif.a, options = list(optimize =
                        3))
snps.from.file          Import SNPs from a BED file or VCF file for use
                        in motifbreakR
snps.from.rsid          Import SNPs from rsid for use in motifbreakR
