# PWM enrichment analysis

## Documentation for package ‘PWMEnrich’ version 4.40.0

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

## Help Pages

A C D E G K L M N P R S T U misc

## -- A --

affinitySequenceSet | Calculate total affinity over a set of sequences
as.data.frame | Convert a MotifEnrichmentReport into a data.frame object
as.data.frame-method | Convert a MotifEnrichmentReport into a data.frame object

## -- C --

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

## -- D --

divideRows | Divide each row of a matrix with a vector
DNAStringSetToList | Convert DNAStringSet to list of DNAString objects

## -- E --

empiricalPvalue | Calculate the empirical P-value by affinity of cutoff.
empiricalPvalueSequenceSet | Empirical P-value for a set of sequences

## -- G --

getBackgroundFrequencies | Get the four nucleotides background frequencies
getPromoters | Get the promoter sequences either for a named organism such as "dm3" or a BSgenome object
gevPerSequence | Apply GEV background normalization per every sequence
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

## -- K --

keepFinite | Replace all infinite values by 0

## -- L --

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

## -- M --

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
makeStartEndPos | Divide total.len into fragments of length len by providing start,end positions
matrixShuffleZscorePerSequence | Obtain z-score for motif column shuffling
maxAligned | Returned the aligned motif parts
motifDiffEnrichment | Differential motif enrichment
motifEcdf | Calculate the empirical distribution score distribution for a set of motifs
motifEnrichment | Motif enrichment
MotifEnrichmentReport-class | A report class with formatted results of motif enrichment
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 or number of hits over a threshold
motifScoresBigMemory | This is a memory intensive version of motifScore() which is about 2 times faster
motifSimilarity | Calculates similarity between two PFMs.

## -- N --

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

## -- P --

PFMtoPWM | Convert frequencies into motifs using PWMUnscaled
plot-method | Plot the motif enrichment report
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
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-class | A class that represents a Position Weight Matrix (PWM)
PWMCutoffBackground-class | Hit count background distribution for a set of PWMs
PWMEmpiricalBackground-class | Background for calculating empirical P-values
PWMGEVBackground-class | Generalized Extreme Values (GEV) background for P-values
PWMLognBackground-class | Lognormal background distribution for a set of PWMs
PWMUnscaled | Create a PWM from PFM

## -- R --

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-method | Reverse complement for the PWM object

## -- S --

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
show-method | show method for MotifEnrichmentReport
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

## -- T --

toPWM | Convert motifs into PWMs
tryAllMotifAlignments | Try all motif alignments and return max score

## -- U --

useBigMemoryPWMEnrich | If to use a faster implementation of motif scanning that requires abount 5 to 10 times more memory

## -- misc --

$-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
.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.seq input parameter
.normargPfm | Input parameter normalization for PWMUnscaled
.normargPriorParams | Input parameter normalization function for PWMUnscaled
[-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