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SIG: new data structures for Bioconductor #8

@lwaldron

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@lwaldron

From @lwaldron on October 22, 2017 4:26

This SIG will discuss recent and needed Bioconductor data classes. Some recent or in-testing data classes to discuss are:

  • MultiAssayExperiment (for "gluing" different types of assays together)
  • RaggedExperiment (for copy number, mutations, or other data represented by different genomic ranges for each sample)
  • restfulSE::RESTfulSummarizedExperiment, restfulSE::BQSummarizedExperiment for remote storage + local interactive analysis of very large datasets

One presently identified need is a Bioconductor class for representing the drug sensitivity data from pharmacogenomics studies such as the Cancer Cell Line Encyclopedia (CCLE) and NCI-60. These studies perform standard -omics assays, but also dose-response experiments where cell lines are subjected to varying doses of each of numerous compounds. Responses are measured as cell viability, and the resulting dose-response curves are summarized using measures such as LC-50. The full dose-response data are a 3-D array (dose x time x cell line), which should be stored in addition to summary measure matrices (e.g. LC-50 concentration x cell line) The PharmacoGx Bioconductor package from the @bhaibeka lab provides numerous curated pharmacogenomics datasets as rich PharmacoSet objects, but these lack the flexibility and novel data storage models that would be available using a SummarizedExperiment-derived object for sensitivity data contained along with -omics assays within a MultiAssayExperiment. Therefore a desired outcome from this SIG is a draft class definition for cell line drug sensitivity data extending from SummarizedExperiment. This would accomplish both a needed new data class, and experience for those participating in extending existing core data structures to novel data types.

Topic leader: Levi Waldron @lwaldron
Scribe: Vincent Carey @vjcitn (Vince can I volunteer you?)

Any interested participants are invited to use the issue to ask questions, suggest other relevant topics for discussion, and/or express their interest in participating.

Copied from original issue: Bioconductor/EuroBioc2017#5

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