PWMEnrich: PWM enrichment analysis

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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.

Author
Robert Stojnic, Diego Diez
Date of publication
None
Maintainer
Robert Stojnic <robert.stojnic@gmail.com>
License
LGPL (>= 2)
Version
4.10.0

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...

Files in this package

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