# PWM enrichment analysis

## Documentation for package ‘PWMEnrich’ version 4.4.0

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

## Help Pages

$-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