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

## Documentation for package ‘motifRG’ version 1.12.0

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

## 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