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PWMEnrich (version 4.8.2)

PWM enrichment analysis

Description

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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Version

Version

4.8.2

License

LGPL (>= 2)

Maintainer

Robert Stojnic

Last Published

February 15th, 2017

Functions in PWMEnrich (4.8.2)

makePWMPvalCutoffBackgroundFromSeq

Construct a P-value cutoff background from a set of sequences

Plotting for the PWM class

PWMCutoffBackground

Hit count background distribution for a set of PWMs

PWMLognBackground

Lognormal background distribution for a set of PWMs

useBigMemoryPWMEnrich

If to use a faster implementation of motif scanning that requires abount 5 to 10 times more memory

MotifEnrichmentResults

A wrapper class for results of motifEnrichment() that should make it easier to access the results.

A class that represents a Position Weight Matrix (PWM)

Calculate the empirical distribution score distribution for a set of motifs

Scan the whole sequence on both strands

makePWMCutoffBackground

Make a cutoff background

makePWMGEVBackground

Make a GEV background distribution

Convert motifs into PWMs

[,PWMLognBackground-method

Get the background for a subset of PWMs

names,PWMEmpiricalBackground

Names of variables

Make priors from background sequences

plotMultipleMotifs

Plot mulitple motifs in a single plot

Motif affinity of number of hits over a threshold

registerCoresPWMEnrich

Register than PWMEnrich can use parallel CPU cores

names,PWMGEVBackground

Names of variables

plotTopMotifsSequence,MotifEnrichmentResults-method

Plot the top N enrichment motifs in a single sequence

motifRankingForSequence,MotifEnrichmentResults-method

Get a ranking of motifs by their enrichment in one specific sequence

makePWMEmpiricalBackground

Make an empirical P-value background

[,PWMEmpiricalBackground-method

Get the background for a subset of PWMs

motifRankingForGroup,MotifEnrichmentResults-method

Get a ranking of motifs by their enrichment in the whole set of sequences

Convert frequencies into motifs using PWMUnscaled

getBackgroundFrequencies

Get the four nucleotides background frequencies

Read in motifs in JASPAR or TRANSFAC format

Make a background for a set of position frequency matrices

makePWMLognBackground

Make a lognormal background distribution

motifDiffEnrichment

Differential motif enrichment

MotifEnrichmentReport

A report class with formatted results of motif enrichment

[,PWMCutoffBackground-method

Get the background for a subset of PWMs

Information content for a PWM or PFM

plotMotifScores

Plot the raw motifs scores as returned by motifScores()

groupReport,MotifEnrichmentResults-method

Generate a motif enrichment report for the whole group of sequences together

motifEnrichment

Motif enrichment

sequenceReport,MotifEnrichmentResults-method

Generate a motif enrichment report for a single sequence

reverseComplement

Reverse complement for the PWM object

as.data.frame,MotifEnrichmentReport-method

Convert a MotifEnrichmentReport into a data.frame object

names,MotifEnrichmentResults

Names of variables

plotTopMotifsGroup,MotifEnrichmentResults-method

Plot the top N enrichment motifs in a group of sequences

names,PWMLognBackground

Names of variables

PWMEmpiricalBackground

Background for calculating empirical P-values

makePWMPvalCutoffBackground

Construct a cutoff background from empirical background

names,MotifEnrichmentReport

Names of variables

motifSimilarity

Calculates similarity between two PFMs.

names,PWMCutoffBackground

Names of variables

Draw a motif logo on an existing viewport

Names of variables

[,PWMGEVBackground-method

Get the background for a subset of PWMs

PWMGEVBackground

Generalized Extreme Values (GEV) background for P-values

Create a PWM from PFM