binding_sites: motif hits on the foreground sequences
In cobindR: Finding Co-occuring motifs of transcription factor binding sites

Description Usage Arguments Value Author(s) See Also Examples

motif hits on the foreground sequences

## S4 method for signature 'cobindr'
binding_sites(x)
## S4 replacement method for signature 'cobindr,data.frame'
binding_sites(x) <- value

`x`	a cobindr object
`value`	data.frame holding the binding site hits in the foreground sequences

motif hits in foreground sequences as data.frame

Rob Lehmann <r.lehmann@biologie.hu-berlin.de>

uid,name,sequences,bg_sequences,desc,configuration,binding_sites,bg_binding_sites,pfm,pairs,bg_pairs,pairs_of_interest

cfg <- cobindRConfiguration()
sequence_type(cfg) <- 'fasta'
sequence_source(cfg) <- system.file('extdata/sox_oct_example_vignette_seqs.fasta',package='cobindR')
sequence_origin(cfg) <- 'Mouse Embryonic Stem Cell Example ChIP-Seq Oct4 Peak binding_sites'
cbr <- cobindr(cfg)
binding_sites(cbr)