Identification of putative mammalian orthologs to given enhancer

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Documentation for package ‘enhancerHomologSearch’ version 1.6.1

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

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$-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"'