# A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

## Documentation for package ‘motifbreakR’ version 2.0.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

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