# DiffLogo: A comparative visualisation of biooligomer motifs

## Documentation for package ‘DiffLogo’ version 2.8.0

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

## 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.