PWM enrichment analysis


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Documentation for package ‘PWMEnrich’ version 2.2.0

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$-method Names of variables
$-method Names of variables
$-method Names of variables
$-method Names of variables
$-method Names of variables
$-method Names of variables
.inputParamMotifs Normalizes the motifs input argument for multiple functions...
.inputParamSequences Normalize the sequences input argument...
.inputPFMfromMatrixOrPWM Check the frequency matrix input parameter for motifSimilarity...
.normalize.bg.seq check consistency of bg...
.normargPfm Input parameter normalization for PWMUnscaled...
.normargPriorParams Input parameter normalization function for PWMUnscaled...
affinitySequenceSet Calculate total affinity over a set of sequences...
cloverPvalue1seq Calculate the Clover P-value as described in the Clover paper...
cloverScore Calculate the Clover score using the recursive formula from Frith et al...
colMedians Calculate medians of columns...
colSds Calculate standard deviations of columns...
concatenateSequences Concatenata DNA sequences into a single character object...
cutoffZscore Z-score calculation for cutoff hits...
cutoffZscoreSequenceSet Z-score calculation for cutoff hits for group of sequences...
divideRows Divide each row of a matrix with a vector...
DNAStringSetToList Convert DNAStringSet to list of DNAString objects...
empiricalPvalue Calculate the empirical P-value by affinity of cutoff.
empiricalPvalueSequenceSet Empirical P-value for a set of sequences...
getBackgroundFrequencies Get the four nucleotides background frequencies...
gevPerSequence Apply GEV background normalization per every sequence...
keepFinite Replace all infinite values by 0...
length Names of variables
length-method Names of variables
logNormPval Calculate the P-value from lognormal distribution with background of equal length...
logNormPvalSequenceSet Lognormal P-value for a set of sequences...
makeBackground Make a background for a set of position frequency matrices...
makePriors Make priors from background sequences...
makePWMCutoffBackground Make a cutoff background...
makePWMEmpiricalBackground Make an empirical P-value background...
makePWMGEVBackground Make a GEV background distribution...
makePWMLognBackground Make a lognormal background distribution...
makePWMPvalCutoffBackground Construct a cutoff background from empirical background...
makeStartEndPos Divide total...
matrixShuffleZscorePerSequence Obtain z-score for motif column shuffling...
maxAligned Returned the aligned motif parts...
motifDiffEnrichment Differential motif enrichment
motifEnrichment Motif enrichment
MotifEnrichmentResults A wrapper class for results of motifEnrichment() that should make it easier to access the results.
MotifEnrichmentResults-class A wrapper class for results of motifEnrichment() that should make it easier to access the results.
motifIC Information content for a PWM or PFM...
motifPrAUC Calculate PR-AUC for motifs ranked according to some scoring scheme...
motifRankingForGroup Get a ranking of motifs by their enrichment in the whole set of sequences...
motifRankingForGroup-method Get a ranking of motifs by their enrichment in the whole set of sequences...
motifRankingForSequence Get a ranking of motifs by their enrichment in one specific sequence...
motifRankingForSequence-method Get a ranking of motifs by their enrichment in one specific sequence...
motifRecoveryAUC Calculate Recovery-AUC for motifs ranked according to some scoring scheme...
motifScores Motif affinity of number of hits over a threshold...
motifScoresBigMemory This is a memory intensive version of motifScore() which is abount 2 times faster...
motifSimilarity Calculates similarity between two PFMs.
names-method Names of variables
names-method Names of variables
names-method Names of variables
names-method Names of variables
names-method Names of variables
names-method Names of variables
PFMtoPWM Convert frequencies into motifs using PWMUnscaled...
pickGenome A helper function to pick a genome for an organism...
plot Plotting for the PWM class...
plot-method Plotting for the PWM class...
plotMultipleMotifs Plot mulitple motifs in a single plot...
plotPFM Plot a PFM (not PWM) using seqLogo...
plotTopMotifsGroup Plot the top N enrichment motifs in a group of sequences...
plotTopMotifsGroup-method Plot the top N enrichment motifs in a group of sequences...
plotTopMotifsSequence Plot the top N enrichment motifs in a single sequence...
plotTopMotifsSequence-method Plot the top N enrichment motifs in a single sequence...
PWM A class that represents a Position Weight Matrix (PWM)...
PWM-class A class that represents a Position Weight Matrix (PWM)...
PWMCutoffBackground Hit count background distribution for a set of PWMs...
PWMCutoffBackground-class Hit count background distribution for a set of PWMs...
PWMEmpiricalBackground Background for calculating empirical P-values...
PWMEmpiricalBackground-class Background for calculating empirical P-values...
PWMGEVBackground Generalized Extreme Values (GEV) background for P-values...
PWMGEVBackground-class Generalized Extreme Values (GEV) background for P-values...
PWMLognBackground Lognormal background distribution for a set of PWMs...
PWMLognBackground-class Lognormal background distribution for a set of PWMs...
PWMUnscaled Create a PWM from PFM
rankingProcessAndReturn A helper function for motifRankingForGroup and motifRankingForSequence with the common code...
readJASPAR Read motifs in JASPAR format...
readMotifs Read in motifs in JASPAR or TRANSFAC format...
readTRANSFAC Read in motifs in TRANSFAC format...
registerCoresPWMEnrich Register than PWMEnrich can use parallel CPU cores...
reverseComplement Reverse complement for the PWM object...
reverseComplement-method Reverse complement for the PWM object...
scanWithPWM Scan the whole sequence on both strands...
seqLogoGrid Draw a motif logo on an existing viewport...
show-method show method for MotifEnrichmentResults...
show-method show method for PWM...
show-method show method for PWMCutoffBackground...
show-method show method for PWMEmpiricalBackground...
show-method show method for PWMGEVBackground...
show-method show method for PWMLognBackground...
tryAllMotifAlignments Try all motif alignments and return max score...
useBigMemoryPWMEnrich If to use a faster implementation of motif scanning that requires abount 5 to 10 times more memory...