Package: methylprep
methylprepis a python package for processing Illumina methylation array data.
View onReadTheDocs.Methylprep is part of the methylsuitemethylprepis part of themethylsuiteof python packages that provide functions to process and analyze DNA methylation data from Illumina's Infinium arrays (27k, 450k, and EPIC, as well as mouse arrays). Themethylpreppackage contains functions for processing raw data files from arrays and downloading/processing public data sets from GEO (the NIH Gene Expression Omnibus database repository), or from ArrayExpress. It contains both a command line interface (CLI) for processing data from local files, and a set of functions for building a custom pipeline in a jupyter notebook or python scripting environment. The aim is to offer a standard process, with flexibility for those who want it.methylprepdata processing has also been tested and benchmarked to match the outputs of two popular R packages:sesame(v1.10.4) andminfi(v1.38).Methylsuite package componentsYou should install all three components, as they work together. The parts include:methylprep: (this package) for processingidatfiles or downloading GEO datasets from NIH. Processing steps includeinfer type-I channel switchNOOB (normal-exponential convolution on out-of-band probe data)poobah (p-value with out-of-band array hybridization, for filtering lose signal-to-noise probes)qualityMask (to exclude historically less reliable probes)nonlinear dye bias correction (AKA signal quantile normalization between red/green channels across a sample)calculate beta-value, m-value, or copy-number matrixlarge batch memory management, by splitting it up into smaller batches during processingmethylcheck: for quality control (QC) and analysis, includingfunctions for filtering out unreliable probes, based on the published literatureNote thatmethylprep processwill exclude a set of unreliable probes by default. You can disable that using the --no_quality_mask option from CLI.sample outlier detectionarray level QC plots, based on Genome Studio functionsa python clone of Illumina's Bead Array Controls Reporter software (QC)data visualization functions based onseabornandmatplotlibgraphic libraries.predict sex of human samples from probesinteractive method for assigning samples to groups, based on array data, in a Jupyter notebookmethylizeprovides more analysis and interpretation functionsdifferentially methylated probe statistics (between treatment and control samples)volcano plots (which probes are the most different?)manhattan plots (where in genome are the differences?)Installationmethylprepmaintains configuration files for your Python package manager of choice:pipenvorpip. Conda install is coming soon.>>>pipinstallmethylprepor if you want to install all three packages at once:>>>pipinstallmethylsuiteTutorials and GuidesIf you're new to DNA methylation analysis, we recommend reading throughthis introductionin order get the background knowledge needed to best utilizemethylprepeffectively. Otherwise, you're ready to usemethylprepfor:processingyour own methylation datadownloadingunprocessed data(like IDAT files) from GEO.downloadingpreprocessed data(like beta values) from GEO.building a composite datasetusing control samplesfrom GEO.building a composite dataset from GEO datawith any keyword you choose(e.g. combining all GEO datasets that have methylation data from patients with brain cancer).