binding_sites {cobindR} | R Documentation

## motif hits on the foreground sequences

### Description

motif hits on the foreground sequences

### Usage

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

### Arguments

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

### Value

motif hits in foreground sequences as data.frame

### Author(s)

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

### See Also

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

### Examples

    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)

[Package cobindR version 1.20.0 Index]