PWMEnrich: PWM enrichment analysis

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.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("PWMEnrich")
AuthorRobert Stojnic, Diego Diez
Bioconductor views MotifAnnotation SequenceMatching Software
Date of publicationNone
MaintainerRobert Stojnic <robert.stojnic@gmail.com>
LicenseLGPL (>= 2)
Version4.10.0

View on Bioconductor

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

as.data.frame Man page
as.data.frame,MotifEnrichmentReport-method Man page
getBackgroundFrequencies Man page
groupReport Man page
groupReport,MotifEnrichmentResults-method Man page
length Man page
length,PWM-method Man page
makeBackground Man page
makePriors Man page
makePWMCutoffBackground Man page
makePWMEmpiricalBackground Man page
makePWMGEVBackground Man page
makePWMLognBackground Man page
makePWMPvalCutoffBackground Man page
makePWMPvalCutoffBackgroundFromSeq Man page
motifDiffEnrichment Man page
motifEcdf Man page
motifEnrichment Man page
MotifEnrichmentReport Man page
MotifEnrichmentReport-class Man page
[,MotifEnrichmentReport-method Man page
$,MotifEnrichmentReport-method Man page
MotifEnrichmentResults Man page
MotifEnrichmentResults-class Man page
$,MotifEnrichmentResults-method Man page
motifIC Man page
motifRankingForGroup Man page
motifRankingForGroup,MotifEnrichmentResults-method Man page
motifRankingForSequence Man page
motifRankingForSequence,MotifEnrichmentResults-method Man page
motifScores Man page
motifSimilarity Man page
names,MotifEnrichmentReport Man page
names,MotifEnrichmentReport-method Man page
names,MotifEnrichmentResults Man page
names,MotifEnrichmentResults-method Man page
names,PWM 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
names,PWM-method Man page
PFMtoPWM Man page
plot Man page
plot,MotifEnrichmentReport,missing-method Man page
plotMotifScores Man page
plotMultipleMotifs Man page
plot,PWM,missing-method Man page
plotTopMotifsGroup Man page
plotTopMotifsGroup,MotifEnrichmentResults-method Man page
plotTopMotifsSequence Man page
plotTopMotifsSequence,MotifEnrichmentResults-method Man page
PWM Man page
PWM-class Man page
PWMCutoffBackground Man page
PWMCutoffBackground-class Man page
[,PWMCutoffBackground-method Man page
$,PWMCutoffBackground-method Man page
PWMEmpiricalBackground Man page
PWMEmpiricalBackground-class Man page
[,PWMEmpiricalBackground-method Man page
$,PWMEmpiricalBackground-method Man page
PWMGEVBackground Man page
PWMGEVBackground-class Man page
[,PWMGEVBackground-method Man page
$,PWMGEVBackground-method Man page
PWMLognBackground Man page
PWMLognBackground-class Man page
[,PWMLognBackground-method Man page
$,PWMLognBackground-method Man page
$,PWM-method Man page
PWMUnscaled Man page
readMotifs Man page
registerCoresPWMEnrich Man page
reverseComplement Man page
reverseComplement,PWM-method Man page
scanWithPWM Man page
seqLogoGrid Man page
sequenceReport Man page
sequenceReport,MotifEnrichmentResults-method Man page
toPWM Man page
useBigMemoryPWMEnrich Man page

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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