homer {motifbreakR} | R Documentation

## MotifDb object containing motif information from motif databases included in HOMER.

### Description

From the website: "Homer includes several motif databases that are used to help annotate results and conduct searches for known motifs. HOMER contains a custom motif database based on independent analysis of mostly ChIP-Seq data sets which is heavily utilized in the software." See http://homer.salk.edu/homer/motif/motifDatabase.html for more information on how these files were generated, and Homer's sources.

### Usage

    homer

### Format

`MotifDb` object of length 247; to access metadata use mcols(homer)

providerName

  Name provided HOMER

providerId

  Factor Name provided by HOMER

dataSource

  `"HOMER"`

geneSymbol

  Symbol provided by HOMER

geneId

  Entrez gene id for the transcription factor

geneIdType

  `"ENTREZ"`

proteinId

  UNIPROT id for the transcription factor

proteinIdType

  `"UNIPROT"`

organism

  `"Hsapiens"`

sequenceCount

  `NA`

bindingSequence

  Consensus sequence for the motif

bindingDomain

  DBD provided by HOMER

tfFamily

  `NA`

experimentType

  The Celltype, IP, Assay, and GEO id if applicable for the motif

pubmedID

  `"20513432"` see `Source` for more details

### Details

Load with `data(homer)`

### Value

`MotifList-class` object

### Source

Heinz S, Benner C, Spann N, Bertolino E et al. (2010 May 28) Simple Combinations of Lineage-Determining Transcription Factors Prime cis-Regulatory Elements Required for Macrophage and B Cell Identities. Mol Cell, 38(4):576-589. PMID: 20513432

### See Also

http://homer.salk.edu/homer/index.html http://homer.salk.edu/homer/motif/motifDatabase.html http://homer.salk.edu/homer/motif/HomerMotifDB/homerResults.html

### Examples

    data(homer)
    homer

[Package motifbreakR version 2.4.0 Index]