Overview of the PWMEnrich package

The main functionality of the package is Position Weight Matrix (PWM) enrichment analysis in a single sequence (e.g. enhancer of interest) or a set of sequences (e.g. set of ChIP-chip/seq peaks). Note that this is not the same as de-novo motif finding which discovers novel motifs, nor motif comparison which aligns motifs. The package is built upon Biostrings and offers high-level functions to scan for DNA motif occurrences and compare them against a genomic background. There are multiple packages with pre-compiled genomic backgrounds such as PWMEnrich.Dmelanogaster.background, PWMEnrich.Hsapiens.background and PWMEnrich.Mmusculus.background. In these packages the genomic distribution is calculated for motifs from the MotifDb database. The PWMEnrich package contains all the functions used to create these packages, so you can calculate your own background distributions for your own set of motifs. In this vignette we will use the Drosophila package, but the other background packages are used in the same way (see Section 5 for minor human-specific differences). ∗e-mail: [email protected], Cambridge Systems Biology Institute, University of Cambridge, UK 1In this vignette we use ”PWM”, ”DNA motif” and ”motif” interchangeably.