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


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Documentation for package ‘motifbreakR’ version 1.4.0

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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
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