# Identification of putative mammalian orthologs to given enhancer

## Documentation for package ‘enhancerHomologSearch’ version 1.6.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

$-method | Class '"Enhancers"'
$<--method | Class '"Enhancers"'
alignment | Output
alignmentOne | Get alignment scores
coerce | Class '"Enhancers"'
coerce-method | Class '"Enhancers"'
conservedMotifs | check the conserved motifs in the orthologs
distance | Class '"Enhancers"'
distance-method | Class '"Enhancers"'
distance<- | Class '"Enhancers"'
distance<--method | Class '"Enhancers"'
Enhancers | Class '"Enhancers"'
Enhancers-class | Class '"Enhancers"'
genome | Class '"Enhancers"'
genome-method | Class '"Enhancers"'
genome<- | Class '"Enhancers"'
genome<--method | Class '"Enhancers"'
getENCODEdata | Download enhancer sequences from ENCODE
getSeq-method | Class '"Enhancers"'
motifs | Pre-clustered motifs from human and mouse
peaks | Class '"Enhancers"'
peaks-method | Class '"Enhancers"'
peaks<- | Class '"Enhancers"'
peaks<--method | Class '"Enhancers"'
queryEncode | query data from ENCODE by predefined criteria
query_tfbp | Class '"Enhancers"'
query_tfbp-method | Class '"Enhancers"'
saveAlignments | output alignments
searchTFBPS | Transcription Factor Binding Pattern Similarity (TFBPS) search
seqinfo-method | Class '"Enhancers"'
show-method | Class '"Enhancers"'
shuffle | shuffle reads
subset-method | Class '"Enhancers"'
subsetByOverlaps-method | Class '"Enhancers"'
subsetByOverlpas-method | Class '"Enhancers"'
tfbp | Class '"Enhancers"'
tfbp-method | Class '"Enhancers"'