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yocra3 / epimutacions

Package to detect epimutations from DNA methylation data
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Task 15. Identify other data sources for development and testing #31

Open carleshf opened 4 years ago

yocra3 commented 4 years ago

The package needs some data for testing. Two different datasets are required:

yocra3 commented 4 years ago

Data for testing and examples consist of a very simple dataset that will exemplify the functions included in the package. This data does not have a biological meaning but it is meant to show how the package works (examples) and to check that code changes does not break the package (test). Therefore, it should be prioritized having a reduced dataset rather than a real dataset. Two datasets should be created:

  1. A matrix of methylation values: this matrix represents a small example DNA methylation matrix and will be used to test functions calling outliers. For instance, it can be comprised of 5 samples (columns) and 10 rows (CpGs). The first sample might be the proband who has a different methylation pattern from the rest. Methylation values are expressed in betas, so they range between 0 and 1.
  2. A GenomicRatioSet: This object can be used to test the main function. This object will contain as measurements matrix 1 plus additional information of individuals (i.e. age, sex,...) and probes (i.e. chromosome, position...).
yocra3 commented 4 years ago

Data for evaluating the methods consist of public data where we can evaluate our algorithm.