Reference

All functions

Enhancers() `$`(<Enhancers>) `$<-`(<Enhancers>) distance(<Enhancers>,<ANY>) `distance<-`(<Enhancers>) tfbp(<Enhancers>) query_tfbp(<Enhancers>) getSeq(<Enhancers>) subsetByOverlaps(<Enhancers>,<ANY>) subset(<Enhancers>) seqinfo(<Enhancers>) genome(<Enhancers>) `genome<-`(<Enhancers>) peaks(<Enhancers>) `peaks<-`(<Enhancers>) show(<Enhancers>)

Class "Enhancers"

alignment()

Output

alignmentOne()

Get alignment scores

conservedMotifs()

check the conserved motifs in the orthologs

getENCODEdata()

Download enhancer sequences from ENCODE

motifs

Pre-clustered motifs from human and mouse

queryEncode()

query data from ENCODE by predefined criteria

saveAlignments()

output alignments

searchTFBPS()

Transcription Factor Binding Pattern Similarity (TFBPS) search

shuffle()

shuffle reads