Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

Documentation for package ‘motifStack’ version 1.44.1

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Plot stacked logos for single or multiple DNA, RNA and amino acid sequence

-- A --

-- B --

browseMotifs	browse motifs
browseMotifs-shiny	Shiny bindings for browseMotifs
browseMotifsOutput	Shiny bindings for browseMotifs

-- C --

calF	calculate frequence
calI	calculate I'
clusterMotifs	cluster motifs
coerce	Class '"pfm"'
coerce()	Class '"pssm"'
coerce-method	Class '"pcm"'
coerce-method	Class '"pfm"'
coerce-method	Class '"psam"'
coerce-method	Class '"pssm"'
colorset	retrieve color setting for logo
compare2profiles	compare two profiles
compareProfiles	comapre w pcm

-- D --

DNAmotifAlignment	align DNA motifs
DNAmotifToRNAmotif	convert DNA motif into RNA motif
dpGlobal	Global alignment version
dpLocal	Dynamic programming function, local version

-- F --

-- G --

GeomMotif	GeomMotif object
geom_motif	geom_motif
getALLRscoreFromCounts	calculate ALLR from counts
getDistance	Calculate distances between two profiles
getIC	Class '"pcm"'
getIC-method	Class '"pcm"'
getIC-method	Class '"pfm"'
getRankedUniqueMotifs	get the unique motif in each category grouped by distance
getScore	Calculate pair_wise position score

-- H --

add alpha transparency value to a color

-- I --

import motifs from local files

-- M --

marker	Class 'marker'
marker-class	Class 'marker'
matalign	Matrix Aligner
matrixReverseComplement	Class '"pcm"'
matrixReverseComplement-method	Class '"pcm"'
matrixReverseComplement-method	Class '"pfm"'
matrixReverseComplement-method	Class '"psam"'
matrixReverseComplement-method	Class '"pssm"'
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
motifSig	Class '"motifSig"'
motifSig-class	Class '"motifSig"'
motifSignature	get signatures from motifs
motifStack	plot a DNA sequence logo stack

-- N --

nodelist	Class '"motifSig"'
nodelist-method	Class '"motifSig"'

-- O --

ouNode	Class 'ouNode'
ouNode-class	Class 'ouNode'

-- P --

pcm	Class '"pcm"'
pcm-class	Class '"pcm"'
pcm2pfm	Class '"pcm"'
pcm2pfm-method	Class '"pcm"'
pcm2pssm	Class '"pcm"'
pcm2pssm-method	Class '"pcm"'
pfm	Class '"pfm"'
pfm-class	Class '"pfm"'
pfm2pwm	convert pfm object to PWM
plot	Class '"pcm"'
plot-method	Class '"pcm"'
plot-method	Class '"pfm"'
plot-method	Class '"psam"'
plot-method	Class '"pssm"'
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	Class '"psam"'
psam-class	Class '"psam"'
pssm	Class '"pssm"'
pssm-class	Class '"pssm"'

-- R --

readPCM	read pcm from a path
renderbrowseMotifs	Shiny bindings for browseMotifs
reorderUPGMAtree	re-order UPGMA tree

-- S --

-- T --

-- misc --

$-method	Class 'marker'
$-method	Class '"motifSig"'
$-method	Class 'ouNode'
$-method	Class '"pcm"'
$-method	Class '"pfm"'
$-method	Class '"psam"'
$-method	Class '"pssm"'
$<--method	Class 'marker'
$<--method	Class '"motifSig"'
$<--method	Class 'ouNode'
$<--method	Class '"pcm"'
$<--method	Class '"pfm"'
$<--method	Class '"psam"'
$<--method	Class '"pssm"'
_PACKAGE	Plot stacked logos for single or multiple DNA, RNA and amino acid sequence