PWM enrichment analysis


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Documentation for package ‘PWMEnrich’ version 4.32.0

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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