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gabrielodom / pathwayPCA

integrative pathway analysis with modern PCA methodology and gene selection
https://gabrielodom.github.io/pathwayPCA/
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Add more realistic data to the package #7

Closed gabrielodom closed 6 years ago

gabrielodom commented 6 years ago

In an effort to beef up the examples, we are going to add a newer .gmt file (from Alex Pico) and a new pheno + assay data set (from Suhas Vasaikar of the Bing Zhang Lab).

gabrielodom commented 6 years ago

I've added and documented the pathwaySet from Alex. I had to change pathways 147 and 353 because their descriptions contained Greek letters. Each Greek letter has been replaced by its name in all caps; e.g. $\beta$ replaced by BETA.

gabrielodom commented 6 years ago

After emailing Alex and Steven, we will have the new pathwaySet objects to add to the package soon. Steven is also emailing Suhas to remind him to send us breast, colon, and lung cancer data sets (but we will not add these to the package). We will use these data sets for some examples in the software paper and the more advanced vignette.

gabrielodom commented 6 years ago

James and I have worked on cleaning and analyzing the four data sets from Suhas and the pathway set from Alex. We will use the PNNL ovarian cancer data set combined with the cleaned Wikipathways pathway set in gene symbol form.

gabrielodom commented 6 years ago

This issue will be fixed when we merge the devel branch to the master branch.