Function reference • motiftools

All functions
`show(<MotifCompareResult>)` `nquery()` `ntarget()`	MotifCompareResult-class
`show(<MotifSearchResult>)` `[`(<MotifSearchResult>,<ANY>) `nmotif()` `nseq()` `motifNames()` `sequenceNames()` `scores()` `pwm()`	MotifSearchResult-class
`align()`	Align two sequences
`conservationMatrix()`	Compute the conservation score matrix from a MSA
`dcor()`	dcor
`eud()`	Euclidean distance
`getMotifArchSimilarity()`	getMotifArchSimilarity
`getMotifArchString()`	getMotifArchString
`getMotifCoverage()`	getMotifCoverage
`getMotifMatrix()`	getMotifMatrix
`getMotifSimilarity()`	getMotifSimilarity
`getMotifTotalCoverage()`	getMotifTotalCoverage
`getMotifsBySeq()`	getMotifsBySeq
`motifAlign()`	Align two motifs represented as PWMs
`plotConservationMatrix()`	Plots a heatmap with the conservation score for each residue
`plotMotifArchSimilarity()`	plotMotifArchSimilarity
`plotMotifMatches()`	plotMotifMatches
`plotMotifMatrix()`	plotMotifMatrix
`readFIMO()`	Read results from FIMO motif search stored in XML format.
`readMAST()`	Read results from MAST motif search stored in XML format.
`readMEME()`	Read results from MEME motif search stored in XML format.
`readTOMTOM()`	readTOMTOM

Reference