PWMEnrich: PWM enrichment analysis
Version 4.12.0

A toolkit of high-level functions for DNA motif scanning and enrichment analysis built upon Biostrings. The main functionality is PWM enrichment analysis of already known PWMs (e.g. from databases such as MotifDb), but the package also implements high-level functions for PWM scanning and visualisation. The package does not perform "de novo" motif discovery, but is instead focused on using motifs that are either experimentally derived or computationally constructed by other tools.

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AuthorRobert Stojnic, Diego Diez
Bioconductor views MotifAnnotation SequenceMatching Software
Date of publicationNone
MaintainerRobert Stojnic <robert.stojnic@gmail.com>
LicenseLGPL (>= 2)
Version4.12.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PWMEnrich")

Man pages

as.data.frame-commaMotifEnrichmentReport-method: Convert a MotifEnrichmentReport into a data.frame object
getBackgroundFrequencies: Get the four nucleotides background frequencies
groupReport-commaMotifEnrichmentResults-method: Generate a motif enrichment report for the whole group of...
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...
motifEnrichment: Motif enrichment
MotifEnrichmentReport: A report class with formatted results of motif enrichment
MotifEnrichmentResults: A wrapper class for results of motifEnrichment() that should...
motifIC: Information content for a PWM or PFM
motifRankingForGroup-commaMotifEnrichmentResults-method: Get a ranking of motifs by their enrichment in the whole set...
motifRankingForSequence-commaMotifEnrichmentResults-method: Get a ranking of motifs by their enrichment in one specific...
motifScores: Motif affinity of number of hits over a threshold
motifSimilarity: Calculates similarity between two PFMs.
operators-MotifEnrichmentReport: Names of variables
operators-MotifEnrichmentResults: Names of variables
operators-PWM: Names of variables
operators-PWMCutoffBackground: Names of variables
operators-PWMEmpiricalBackground: Names of variables
operators-PWMGEVBackground: Names of variables
operators-PWMLognBackground: Names of variables
PFMtoPWM: Convert frequencies into motifs using PWMUnscaled
plot: Plotting for the PWM class
plotMotifScores: Plot the raw motifs scores as returned by motifScores()
plotMultipleMotifs: Plot mulitple motifs in a single plot
plotTopMotifsGroup-commaMotifEnrichmentResults-method: Plot the top N enrichment motifs in a group of sequences
plotTopMotifsSequence-commaMotifEnrichmentResults-method: Plot the top N enrichment motifs in a single sequence
PWM: A class that represents a Position Weight Matrix (PWM)
PWMCutoffBackground: Hit count background distribution for a set of PWMs
PWMEmpiricalBackground: Background for calculating empirical P-values
PWMGEVBackground: Generalized Extreme Values (GEV) background for P-values
PWMLognBackground: 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
scanWithPWM: Scan the whole sequence on both strands
seqLogoGrid: Draw a motif logo on an existing viewport
sequenceReport-commaMotifEnrichmentResults-method: Generate a motif enrichment report for a single sequence
subsetting-PWMCutoffBackground: Get the background for a subset of PWMs
subsetting-PWMEmpiricalBackground: Get the background for a subset of PWMs
subsetting-PWMGEVBackground: Get the background for a subset of PWMs
subsetting-PWMLognBackground: Get the background for a subset of PWMs
toPWM: Convert motifs into PWMs
useBigMemoryPWMEnrich: If to use a faster implementation of motif scanning that...

Functions

$,MotifEnrichmentReport-method Man page
$,MotifEnrichmentResults-method Man page
$,PWM-method Man page
$,PWMCutoffBackground-method Man page
$,PWMEmpiricalBackground-method Man page
$,PWMGEVBackground-method Man page
$,PWMLognBackground-method Man page
DNAStringSetToList Source code
MotifEnrichmentReport Man page
MotifEnrichmentReport-class Man page
MotifEnrichmentResults Man page
MotifEnrichmentResults-class Man page
PFMtoPWM Man page Source code
PWM Man page
PWM-class Man page
PWMCutoffBackground Man page
PWMCutoffBackground-class Man page
PWMEmpiricalBackground Man page
PWMEmpiricalBackground-class Man page
PWMGEVBackground Man page
PWMGEVBackground-class Man page
PWMLognBackground Man page
PWMLognBackground-class Man page
PWMUnscaled Man page Source code
[,MotifEnrichmentReport-method Man page
[,PWMCutoffBackground-method Man page
[,PWMEmpiricalBackground-method Man page
[,PWMGEVBackground-method Man page
[,PWMLognBackground-method Man page
addLetter Source code
affinitySequenceSet Source code
as.data.frame Man page
as.data.frame,MotifEnrichmentReport-method Man page
cloverPvalue1seq Source code
cloverScore Source code
colMedians Source code
colSds Source code
concatenateSequences Source code
cutoffZscore Source code
cutoffZscoreSequenceSet Source code
divideRows Source code
empiricalPvalue Source code
empiricalPvalueSequenceSet Source code
getBackgroundFrequencies Man page Source code
getPromoters Source code
gevPerSequence Source code
groupReport Man page
groupReport,MotifEnrichmentResults-method Man page
keepFinite Source code
length Man page
length,PWM-method Man page
letterA Source code
letterC Source code
letterG Source code
letterT Source code
logNormPval Source code
logNormPvalSequenceSet Source code
makeBackground Man page Source code
makePWMCutoffBackground Man page Source code
makePWMEmpiricalBackground Man page Source code
makePWMGEVBackground Man page Source code
makePWMLognBackground Man page Source code
makePWMPvalCutoffBackground Man page Source code
makePWMPvalCutoffBackgroundFromSeq Man page Source code
makePriors Man page Source code
makeStartEndPos Source code
matrixShuffleZscorePerSequence Source code
maxAligned Source code
motifDiffEnrichment Man page Source code
motifEcdf Man page Source code
motifEnrichment Man page Source code
motifIC Man page Source code
motifPrAUC Source code
motifRankingForGroup Man page
motifRankingForGroup,MotifEnrichmentResults-method Man page
motifRankingForSequence Man page
motifRankingForSequence,MotifEnrichmentResults-method Man page
motifRecoveryAUC Source code
motifScores Man page Source code
motifScoresBigMemory Source code
motifSimilarity Man page Source code
names,MotifEnrichmentReport Man page
names,MotifEnrichmentReport-method Man page
names,MotifEnrichmentResults Man page
names,MotifEnrichmentResults-method Man page
names,PWM Man page
names,PWM-method Man page
names,PWMCutoffBackground Man page
names,PWMCutoffBackground-method Man page
names,PWMEmpiricalBackground Man page
names,PWMEmpiricalBackground-method Man page
names,PWMGEVBackground Man page
names,PWMGEVBackground-method Man page
names,PWMLognBackground Man page
names,PWMLognBackground-method Man page
normalize.bg.seq Source code
normargPfm Source code
normargPriorParams Source code
nputPFMfromMatrixOrPWM Source code
nputParamMotifs Source code
nputParamSequences Source code
plot Man page
plot,MotifEnrichmentReport,missing-method Man page
plot,PWM,missing-method Man page
plotMotifScores Man page Source code
plotMultipleMotifs Man page Source code
plotPFM Source code
plotTopMotifsGroup Man page
plotTopMotifsGroup,MotifEnrichmentResults-method Man page
plotTopMotifsSequence Man page
plotTopMotifsSequence,MotifEnrichmentResults-method Man page
pwm2cons Source code
pwm2ic Source code
rankingProcessAndReturn Source code
readJASPAR Source code
readMotifs Man page Source code
readTRANSFAC Source code
registerCoresPWMEnrich Man page Source code
reverseComplement Man page
reverseComplement,PWM-method Man page
scanWithPWM Man page Source code
seqLogoGrid Man page Source code
sequenceReport Man page
sequenceReport,MotifEnrichmentResults-method Man page
toPWM Man page Source code
tryAllMotifAlignments Source code
useBigMemoryPWMEnrich Man page Source code

Files

.Rinstignore
DESCRIPTION
NAMESPACE
R
R/AllDataClasses.R
R/AllGenerics.R
R/MotifEnrichmentReport-methods.R
R/MotifEnrichmentResults-methods.R
R/PWM-methods.R
R/PWMBackground-methods.R
R/background.R
R/clover.R
R/diff.R
R/misc.R
R/options.R
R/plot.R
R/pwm.R
R/readData.R
R/seqLogoSupp.R
R/similarity.R
build
build/vignette.rds
inst
inst/NEWS
inst/doc
inst/doc/PWMEnrich.R
inst/doc/PWMEnrich.Rnw
inst/doc/PWMEnrich.pdf
inst/extdata
inst/extdata/bg.seq-test.RData
inst/extdata/example.fa
inst/extdata/example.transfac
inst/extdata/jaspar-insecta.jaspar
inst/extdata/pfm_vertebrates.txt
inst/extdata/stripe2.fa
inst/extdata/tinman-early-top20.fa
inst/tests
inst/tests/test_clover.R
inst/tests/test_invalidInput.R
inst/tests/test_motifEnrichment.R
inst/tests/test_similarity.R
man
man/MotifEnrichmentReport.Rd
man/MotifEnrichmentResults.Rd
man/PFMtoPWM.Rd
man/PWM.Rd
man/PWMCutoffBackground.Rd
man/PWMEmpiricalBackground.Rd
man/PWMGEVBackground.Rd
man/PWMLognBackground.Rd
man/PWMUnscaled.Rd
man/as.data.frame-commaMotifEnrichmentReport-method.Rd
man/getBackgroundFrequencies.Rd
man/groupReport-commaMotifEnrichmentResults-method.Rd
man/makeBackground.Rd
man/makePWMCutoffBackground.Rd
man/makePWMEmpiricalBackground.Rd
man/makePWMGEVBackground.Rd
man/makePWMLognBackground.Rd
man/makePWMPvalCutoffBackground.Rd
man/makePWMPvalCutoffBackgroundFromSeq.Rd
man/makePriors.Rd
man/motifDiffEnrichment.Rd
man/motifEcdf.Rd
man/motifEnrichment.Rd
man/motifIC.Rd
man/motifRankingForGroup-commaMotifEnrichmentResults-method.Rd
man/motifRankingForSequence-commaMotifEnrichmentResults-method.Rd
man/motifScores.Rd
man/motifSimilarity.Rd
man/operators-MotifEnrichmentReport.Rd
man/operators-MotifEnrichmentResults.Rd
man/operators-PWM.Rd
man/operators-PWMCutoffBackground.Rd
man/operators-PWMEmpiricalBackground.Rd
man/operators-PWMGEVBackground.Rd
man/operators-PWMLognBackground.Rd
man/plot.Rd
man/plotMotifScores.Rd
man/plotMultipleMotifs.Rd
man/plotTopMotifsGroup-commaMotifEnrichmentResults-method.Rd
man/plotTopMotifsSequence-commaMotifEnrichmentResults-method.Rd
man/readMotifs.Rd
man/registerCoresPWMEnrich.Rd
man/reverseComplement.Rd
man/scanWithPWM.Rd
man/seqLogoGrid.Rd
man/sequenceReport-commaMotifEnrichmentResults-method.Rd
man/subsetting-PWMCutoffBackground.Rd
man/subsetting-PWMEmpiricalBackground.Rd
man/subsetting-PWMGEVBackground.Rd
man/subsetting-PWMLognBackground.Rd
man/toPWM.Rd
man/useBigMemoryPWMEnrich.Rd
tests
tests/test-all.R
vignettes
vignettes/PWMEnrich.Rnw
vignettes/references.bib
PWMEnrich documentation built on May 20, 2017, 10:47 p.m.