Function reference • motifStack

All functions
`AAmotifAlignment()`	align AA motifs
`DNAmotifAlignment()`	align DNA motifs
`DNAmotifToRNAmotif()`	convert DNA motif into RNA motif
`GeomMotif`	GeomMotif object
`browseMotifsOutput()` `renderbrowseMotifs()`	Shiny bindings for browseMotifs
`browseMotifs()`	browse motifs
`calF()`	calculate frequence
`calI()`	calculate I'
`clusterMotifs()`	cluster motifs
`colorset()`	retrieve color setting for logo
`compare2profiles()`	compare two profiles
`compareProfiles()`	comapre w pcm
`dpGlobal()`	Global alignment version
`dpLocal()`	Dynamic programming function, local version
`geom_motif()`	geom_motif
`getALLRscoreFromCounts()`	calculate ALLR from counts
`getDistance()`	Calculate distances between two profiles
`getRankedUniqueMotifs()`	get the unique motif in each category grouped by distance
`getScore()`	Calculate pair_wise position score
`highlightCol()`	add alpha transparency value to a color
`importMatrix()`	import motifs from local files
`$`(<marker>)	Class `marker`
`matalign()`	Matrix Aligner
`mergeMotifs()`	merge multiple motifs
`motifCircos()`	plot sequence logo stacks with a radial phylogenic tree and multiple color rings
`motifCloud()`	plot a DNA sequence logo cloud
`motifGrob()`	Motif Grob
`motifHclust()`	Hierarchical Clustering motifs
`motifPiles()`	plot sequence logo stacks with a linear phylogenic tree and multiple color sets
`signatures()` `frequence()` `nodelist()` `sigColor()` `$`(<motifSig>)	Class `"motifSig"`
`motifSignature()`	get signatures from motifs
`motifStack-package`	Plot stacked logos for single or multiple DNA, RNA and amino acid sequence
`motifStack()`	plot a DNA sequence logo stack
`$`(<ouNode>)	Class `ouNode`
`$`(<pcm>) `plot(<pcm>,<ANY>)` `trimMotif()` `matrixReverseComplement()` `addBlank()` `getIC()` `pcm2pfm()` `pcm2pssm()` `as.data.frame(<pcm>)` `format(<pcm>)`	Class `"pcm"`
`$`(<pfm>) `plot(<pfm>,<ANY>)` `getIC(<pfm>,<ANY>)` `trimMotif(<pfm>,<numeric>)` `matrixReverseComplement(<pfm>)` `addBlank(<pfm>,<numeric>,<logical>)` `as.data.frame(<pfm>)` `format(<pfm>)`	Class `"pfm"`
`pfm2pwm()`	convert pfm object to PWM
`plotAffinityLogo()`	plot affinity logo
`plotMotifLogo()`	plot sequence logo
`plotMotifLogoA()`	plot sequence logo without plot.new
`plotMotifLogoStack()`	plot sequence logos stack
`plotMotifLogoStackWithTree()`	plot sequence logos stack with hierarchical cluster tree
`plotMotifOverMotif()`	plot motif over another motif
`plotMotifStackWithPhylog()`	plot sequence logo stacks with a ape4-style phylogenic tree
`plotMotifStackWithRadialPhylog()`	plot sequence logo stacks with a radial phylogenic tree
`plotXaxis()`	plot x-axis
`plotYaxis()`	plot y-axis
`$`(<psam>) `plot(<psam>,<ANY>)` `matrixReverseComplement(<psam>)` `addBlank(<psam>,<numeric>,<logical>)` `as.data.frame(<psam>)` `format(<psam>)`	Class `"psam"`
`$`(<pssm>) `plot(<pssm>,<ANY>)` `matrixReverseComplement(<pssm>)` `addBlank(<pssm>,<numeric>,<logical>)` `as.data.frame(<pssm>)` `format(<pssm>)`	Class `"pssm"`
`readPCM()`	read pcm from a path
`reorderUPGMAtree()`	re-order UPGMA tree
`traceBackGlobal()`	traceback global
`traceBackLocal()`	traceback local

Reference

All functions