A package for discriminative motif discovery, designed for high throughput sequencing dataset


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Documentation for package ‘motifRG’ version 1.18.0

Help Pages

class:Motif Motif objects
ctcf.motifs CTCF motifs predicted by motifRG
findMotif De-novo discovery of distriminative motifs
findMotifFasta Wrapper function for findMotif using fasta input
findMotifFgBg Wrapper function for findMotif using two sequence datasets
getSequence Fetch genomic sequences from GRanges Object
Motif-class Motif objects
motifHtmlTable create of table of motifs
motifLatexTable create of table of motifs
plotMotif plot motif sequence matches
refinePWMMotif create a PWM (Position Weight Model) model given a initial set of motif matches and input sequences
refinePWMMotifExtend create an extended PWM (Position Weight Model) model given a initial set of motif matches and input sequences
summaryMotif summarize a list of motifs
YY1.control Background for YY1 ChIP-Seq peaks in HepG2
YY1.peak YY1 ChIP-Seq peaks in HepG2