DMRforPairs-package: DMRforPairs package

Description Note Note Author(s) References


Please see the DESCRIPTION file.


DMRforPairs is independent of the platform used to generate the data and the pipeline used to pre-process it. It can be used with any dataset as long as data frames are provided that have one matching row for each of the m probes. The examples provided in the vignette and associated publication focus mainly on data aquired using the Infinium HumanMethylation450 BeadChip (450K) platform. Methods to import an preprocess 450K data have been described extensively (see references below). Normalization and preprocessing are readily available in various pipelines and are not part of DMRforPairs. When assassing regionf containing multiple probes, special care should be taken to normalize for probe type bias (for review, see Wilhelm-Benartzi et al 2013). In the following lists some general pointers are given on how to access the data for DMRforPairs using frequenly used and publically avaliable 450K pipelines. An example on how to process data from the CHARM platform is given in the supplementary data of the original DMRforPairs publication (Rijlaarsdam et al 2014, submitted).


Writing permissions are required in the working directory to use the export and visualization functions of DMRforPairs. Internet access is required to use the annotation features.
The figure below shows the relation between the functions described in this manual.



Martin Rijlaarsdam,


DMRforPairs documentation built on Nov. 8, 2020, 4:52 p.m.