NEWS

---

PWMEnrich 4.5.1

• Convert log(P-values) back to P-values for human using a chi-sq distribution Version 4:
• New algorithm for human backgrounds
• New function: toPWM() that takes both PFMs and PPMs

PWMEnrich 3.5

• After further testing revert back to PWMEnrich 2.x group P-value algorithm
• Introduced group sorting by top motifs

PWMEnrich 3.1.4

• New way of estimating P-value for groups of sequences. Note this will produce different P-values for groups of sequences than PWMEnrich 2.x !

PWMEnrich 2.4.4

• Vignette update and fix naming of columns in the motif enrichment report

PWMEnrich 2.4.2

• Improve promoter selection for human and mouse genomes (duplicates are now disregarded)

PWMEnrich 2.4.0

• Major update with more functions and small bugfixes
• Added sequenceReport() and groupReport() for easier report generation
• Visualise motif scores along a sequence with plotMotifScores()
• Creation of empirical CDFs for motif scores
• Almost complete rewrite of the vignette to emphasize the main use cases
• Converted documenation to roxygen2

PWMEnrich 2.3.2

• Subsetting functions for backgrounds from Diego Diez

PWMEnrich 2.3.1

• Fix a bug with plotTopMotifsSequence() with calling an unknown function
• Implement group.only for all background, not only pval in motifEnrichment()
• New default to plotMultipleMotifs() so the margins are better

PWMEnrich 2.2

• Bioconductor 2.12 release version (same as 2.0.0)

PWMEnrich 2.0.0

• General cleanup of the code with various small optimisations
• A FASTA file name is now also taken as input to motifEnrichment()
• The output of motifEnrichment() is now wrapped into a class MotifEnrichmentResults that provides a number of convenience methods for common tasks like ranking and plotting motifs
• Functions makeBackground() and getBackgroundFrequencies() can now take BSgenome objects as input. Thanks to Diego Diez for suggesting this and providing the code.
• Another version of motifScores() has been implemented that requires large amounts of memory, but is at least 2 times faster than the old motifScores() implementation. Use a new option useBigMemoryPWMEnrich() to switch to this implementation.
• PFMtoPWM now accepts a new parameter seq.count so that MotifDb motifs that are expressed as probabilities instead of frequencies can be easily used.

PWMEnrich 1.3.0

• Bioconductor 2.11 release version

PWMEnrich 1.0.2

• Use core package parallel instead of doMC

PWMEnrich 1.0.1

• Fix a typo in test cases and remove doMC as build dependency

PWMEnrich 1.0.0

• Initial release of the package