motifbreakR_motif: MotifDb object containing motif information from the 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 the motif databases of HOCOMOCO, Homer, FactorBook and ENCODE

Description

This object contains all the MotifList-class objects that were generated for this package. See the individual help sections for hocomoco, homer, factorbook, and encodemotif, for how the data is formatted.

Usage

motifbreakR_motif

Format

MotifDb object of length 2816; to access metadata use mcols(motifbreakR_motif)

Details

Load with data(motifbreakR_motif)

Value

MotifList-class object

Source

Kulakovskiy,I.V., Medvedeva,Y.A., Schaefer,U., Kasianov,A.S., Vorontsov,I.E., Bajic,V.B. and Makeev,V.J. (2013) HOCOMOCO: a comprehensive collection of human transcription factor binding sites models. Nucleic Acids Research, 41, D195–D202.

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

J Wang, J Zhuang, S Iyer, XY Lin, et al. (2012) Sequence features and chromatin structure around the genomic regions bound by 119 human transcription factors. Genome Research, 22 (9), 1798-1812, doi:10.1101/gr.139105.112

Pouya Kheradpour and Manolis Kellis (2013 December 13) Systematic discovery and characterization of regulatory motifs in ENCODE TF binding experiments. Nucleic Acids Research, doi:10.1093/nar/gkt1249

See Also

hocomoco, homer, factorbook, and encodemotif

Examples

data(motifbreakR_motif)
motifbreakR_motif

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