homer: MotifDb object containing motif information from motif...

In Simon-Coetzee/motifBreakR: A Package For Predicting The Disruptiveness Of Single Nucleotide Polymorphisms On Transcription Factor Binding Sites

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

Simon-Coetzee/motifBreakR documentation built on Aug. 6, 2024, 5:17 a.m.