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R code export usability improvements (for integration into EGSEA workflow) #8

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AMChalkie opened this Issue Aug 30, 2017 · 0 comments

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AMChalkie commented Aug 30, 2017

Ideally the output from degust/R code would pipe directly into the EGSEA sample example (or something very similar to it for downstream pathway/gene set analysis), so updating the y object so that it contains all the necessary parts would be quite useful. (https://bioconductor.org/packages/release/bioc/html/EGSEA.html)

This may not be complete but I found these two to start with.

  1. y$E does not contain rownames (needed for EGSEA) (Entrez IDs - but should be whatever the input into degust was would be ideal)
  2. y$targets could also contain $group - again from config showing the sample groups used.
  3. y$genes to contain annotation information as input into degust as description fields.
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