Motif Identification and Validation

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Documentation for package ‘MotIV’ version 1.6.0

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&-method Filters Methods
alignments-class Class "alignments"
combineMotifs Combine Motifs
combineMotifs-method Combine Motifs
cooccurences Motifs Occurences and Co-occurences
exportAsRangedData Export MotIV Results
exportAsTransfacFile Write Transfac Files
exportAsTransfacFile-method Write Transfac Files
exportAsTransfacFile-methods Write Transfac Files
filter Filter Motifs
filter-class Class "filter"
filter-method Filter Motifs
filter-methods Filter Motifs
FOXA Dataset for FOXA1
FOXA1_rGADEM Dataset for FOXA1
gadem Dataset for FOXA1
generateDBScores Database Scores Functions
getGademPWM Recover PWM
getPWM Get PWMs from a motiv object
getPWM-method Get PWMs from a motiv object
getPWM-methods Get PWMs from a motiv object
jaspar Jaspar 2010 Database
jaspar.scores Jaspar 2010 Database
length-method Motiv methods
makePWM Constructing a pwm object
matches-class Class "matches"
motifCutree Clustering PWMs Computation
motifDistances Clustering PWMs Computation
motifHclust Clustering PWMs Computation
motifMatch Motifs Matches Analysis
motiv Motiv methods
motiv-class Class "motiv"
names-method Filters Methods
names-method Motiv methods
names<--method Motiv methods
occurences Motifs Occurences and Co-occurences
plot Plot Motiv
plot-method Plot Motiv
plot-methods Plot Motiv
readDBScores Database Scores Functions
readGademPWMFile Read Gadem File
readPWMfile Read Transfac File
seqLogo Plot a sequence logo for a given position weight matrix
setFilter Set Motif Filter
show-method Filters Methods
show-method Motiv methods
similarity Motiv methods
similarity-method Motiv methods
split-method Split Motiv Object
split-methods Split Motiv Object
summary-method Filters Methods
summary-method Motiv methods
transcriptionFactor-class Transcription Factor Class
trimPWMedge Trim PWM edge
viewAlignments Print Motifs Alignments
viewMotifs Print Identified Motifs
viewMotifs-method Print Identified Motifs
viewMotifs-methods Print Identified Motifs
writeDBScores Database Scores Functions
[-method Motiv methods
|-method Filters Methods