DiffLogo: A comparative visualisation of biooligomer motifs
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Documentation for package ‘DiffLogo’ version 2.26.0
Help Pages
| alignPwmSets | Multiple PWMs alignment |
| Alphabet | built alphabet |
| ASN | ASN alphabet |
| baseDistributionPwm | Generates a PWM |
| calculatePvalue | p-value that two PWM-positions are from the same distribution |
| createDiffLogoObject | DiffLogo object |
| differenceOfICs | normalized information content differences |
| diffLogo | Draw DiffLogo |
| diffLogoFromPwm | Draw DiffLogo from PWM |
| diffLogoTable | Draw DiffLogo-table |
| diffLogoTableConfiguration | Configuration object for diffLogoTable |
| DNA | DNA alphabet |
| drawDiffLogoTable | Draws a table of DiffLogos |
| enrichDiffLogoObjectWithPvalues | Enriches a difflogo object with p-values |
| enrichDiffLogoTableWithPvalues | Enriches a matrix of difflogo objects with p-values |
| extendPwmsFromAlignmentVector | Extend pwms with respect to alignment |
| FULL_ALPHABET | Complete character alphabet |
| getAlphabetFromCharacters | returns the alphabet which fits to the given characters |
| getAlphabetFromSequences | returns the alphabet which fits to the given sequences |
| getPwmFromAlignment | Create PWM from alignment |
| getPwmFromAlignmentFile | generates a pwm from an alignment file |
| getPwmFromFastaFile | generates a pwm from a FASTA file |
| getPwmFromFile | generates a pwm from a file of different formats |
| getPwmFromHomerFile | generates a pwm from a homer file |
| getPwmFromPfmOrJasparFile | generates a pwm from a jaspar file |
| getPwmFromPwmFile | generates a pwm from a pwm file |
| getSequencesFromAlignmentFile | extracts the sequences from an alignment file |
| getSequencesFromFastaFile | extracts the sequences from a FASTA file |
| informationContent | information content |
| localPwmAlignment | Align pwms |
| lossOfAbsICDifferences | the change of information content |
| multipleLocalPwmsAlignment | Multiple PWMs alignment |
| normalizedDifferenceOfProbabilities | normalized probability differences |
| normalizePWM | normalizes the given pwm |
| prepareDiffLogoTable | Prepare a table of difflogo objects |
| probabilities | probabilities |
| pwmDivergence | PWM divergence |
| pwmsDistanceMatrix | Multiple PWMs alignment |
| reverseAlignmentVector | Reverse for alignment vector |
| RNA | RNA alphabet |
| seqLogo | Draw sequence logo |
| shannonDivergence | shannon divergence |
| sumOfAbsICDifferences | sum of absolute information content differences |
| sumOfAbsProbabilityDifferences | sum of absolute probability differences |
| sumProbabilities | sum of probabilities, i.e. 1.0 |
| switchDirection | Switches between 'forward' and 'reverse' |
| twoSetsAveragePwmDivergenceFromAlignmentVector | Average divergence between two sets. |