PWM enrichment analysis


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Documentation for package ‘PWMEnrich’ version 4.23.0

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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
$-method Names of variables
as.data.frame Convert a MotifEnrichmentReport into a data.frame object
as.data.frame-method Convert a MotifEnrichmentReport into a data.frame object
getBackgroundFrequencies Get the four nucleotides background frequencies
groupReport Generate a motif enrichment report for the whole group of sequences together
groupReport-method Generate a motif enrichment report for the whole group of sequences together
length Names of variables
length-method Names of variables
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
makePWMPvalCutoffBackgroundFromSeq Construct a P-value cutoff background from a set of sequences
motifDiffEnrichment Differential motif enrichment
motifEcdf Calculate the empirical distribution score distribution for a set of motifs
motifEnrichment Motif enrichment
MotifEnrichmentReport A report class with formatted results of motif enrichment
MotifEnrichmentReport-class A report class with formatted results of 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
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
motifScores Motif affinity of number of hits over a threshold
motifSimilarity Calculates similarity between two PFMs.
names,MotifEnrichmentReport Names of variables
names,MotifEnrichmentResults Names of variables
names,PWM Names of variables
names,PWMCutoffBackground Names of variables
names,PWMEmpiricalBackground Names of variables
names,PWMGEVBackground Names of variables
names,PWMLognBackground 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
names-method Names of variables
names-method Names of variables
PFMtoPWM Convert frequencies into motifs using PWMUnscaled
plot Plotting for the PWM class
plot-method Plotting for the PWM class
plotMotifScores Plot the raw motifs scores as returned by motifScores()
plotMultipleMotifs Plot mulitple motifs in a single plot
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
readMotifs Read in motifs in JASPAR or 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
sequenceReport Generate a motif enrichment report for a single sequence
sequenceReport-method Generate a motif enrichment report for a single sequence
toPWM Convert motifs into PWMs
useBigMemoryPWMEnrich If to use a faster implementation of motif scanning that requires abount 5 to 10 times more memory
[-method Names of variables
[-method Get the background for a subset of PWMs
[-method Get the background for a subset of PWMs
[-method Get the background for a subset of PWMs
[-method Get the background for a subset of PWMs