Man pages for mgledi/DiffLogo
DiffLogo: A comparative visualisation of biooligomer motifs

alignPwmSetsMultiple PWMs alignment
Alphabetbuilt alphabet
ASNASN alphabet
baseDistributionPwmGenerates a PWM
calculatePvaluep-value that two PWM-positions are from the same distribution
createDiffLogoObjectDiffLogo object
differenceOfICsnormalized information content differences
diffLogoDraw DiffLogo
diffLogoFromPwmDraw DiffLogo from PWM
diffLogoTableDraw DiffLogo-table
diffLogoTableConfigurationConfiguration object for diffLogoTable
DNADNA alphabet
drawDiffLogoTableDraws a table of DiffLogos
enrichDiffLogoObjectWithPvaluesEnriches a difflogo object with p-values
enrichDiffLogoTableWithPvaluesEnriches a matrix of difflogo objects with p-values
extendPwmsFromAlignmentVectorExtend pwms with respect to alignment
FULL_ALPHABETComplete character alphabet
getAlphabetFromCharactersreturns the alphabet which fits to the given characters
getAlphabetFromSequencesreturns the alphabet which fits to the given sequences
getPwmFromAlignmentCreate PWM from alignment
getPwmFromAlignmentFilegenerates a pwm from an alignment file
getPwmFromFastaFilegenerates a pwm from a FASTA file
getPwmFromFilegenerates a pwm from a file of different formats
getPwmFromHomerFilegenerates a pwm from a homer file
getPwmFromPfmOrJasparFilegenerates a pwm from a jaspar file
getPwmFromPwmFilegenerates a pwm from a pwm file
getSequencesFromAlignmentFileextracts the sequences from an alignment file
getSequencesFromFastaFileextracts the sequences from a FASTA file
informationContentinformation content
localPwmAlignmentAlign pwms
lossOfAbsICDifferencesthe change of information content
multipleLocalPwmsAlignmentMultiple PWMs alignment
normalizedDifferenceOfProbabilitiesnormalized probability differences
normalizePWMnormalizes the given pwm
prepareDiffLogoTablePrepare a table of difflogo objects
pwmDivergencePWM divergence
pwmsDistanceMatrixMultiple PWMs alignment
reverseAlignmentVectorReverse for alignment vector
RNARNA alphabet
seqLogoDraw sequence logo
shannonDivergenceshannon divergence
sumOfAbsICDifferencessum of absolute information content differences
sumOfAbsProbabilityDifferencessum of absolute probability differences
sumProbabilitiessum of probabilities, i.e. 1.0
switchDirectionSwitches between 'forward' and 'reverse'
twoSetsAveragePwmDivergenceFromAlignmentVectorAverage divergence between two sets.
mgledi/DiffLogo documentation built on July 11, 2017, 2:12 p.m.