# Motif Identification and Validation

## Documentation for package ‘MotIV’ version 1.40.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

&-method | Filters Methods
alignments-class | Class "alignments"
as.data.frame | Coerce to a Data Frame
as.data.frame-method | Coerce to a Data Frame
as.data.frame-methods | Coerce to a Data Frame
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
seqLogo2 | 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