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.

AuthorRobert Stojnic, Diego Diez
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...

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

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