Man pages for alyst/MotIV
Motif Identification and Validation
| aligns-class | Class "alignments" |
| as.data.frame | Coerce to a Data Frame |
| combineMotifs | Combine Motifs |
| exportAsRangedData | Export MotIV Results |
| exportAsTransfacFile | Write Transfac Files |
| filter | Filter Motifs |
| filter-class | Class "filter" |
| filter-methods | Filters Methods |
| FOXA_rGADEM | Dataset for FOXA1 |
| generateDBScores | Database Scores Functions |
| getGademPWM | Recover PWM |
| getPWM | Get PWMs from a motiv object |
| jaspar | Jaspar 2010 Database |
| makePWM | Constructing a pwm object |
| matches-class | Class "matches" |
| motifDistance | Clustering PWMs Computation |
| motifMatch | Motifs Matches Analysis |
| motifOccurences | Motifs Occurences and Co-occurences |
| motiv-class | Class "motiv" |
| motiv-methods | Motiv methods |
| plot | Plot Motiv |
| readGademPWMFile | Read Gadem File |
| readPWMfile | Read Transfac File |
| seqLogo2 | Plot a sequence logo for a given position weight matrix |
| setFilter | Set Motif Filter |
| split | Split Motiv Object |
| tf-class | Transcription Factor Class |
| trimPWMedge | Trim PWM edge |
| viewAlignment | Print Motifs Alignments |
| viewMotifs | Print Identified Motifs |
