https://github.com/vjcitn/aacrpamphlet

October 2018 pamphlet on Bioconductor:Cancer
https://github.com/vjcitn/aacrpamphlet

Last synced: 4 months ago
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October 2018 pamphlet on Bioconductor:Cancer

• Host: GitHub
• URL: https://github.com/vjcitn/aacrpamphlet
• Owner: vjcitn
• Created: 2018-10-13T14:49:34.000Z (over 6 years ago)
• Default Branch: master
• Last Pushed: 2018-10-13T20:32:16.000Z (over 6 years ago)
• Last Synced: 2025-01-09T13:46:07.079Z (5 months ago)
• Language: TeX
• Size: 16.7 MB
• Stars: 1
• Watchers: 4
• Forks: 0
• Open Issues: 0
• Metadata Files:
  • Readme: README.md

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README

        
# aacrPamphlet

October 2018 pamphlet on Bioconductor:Cancer

# Comments

- The rendered PDF with hyperlinks is ccl.pdf

- You can create it from ccl.Rmd under the following conditions

    - You have sufficient pandoc infrastructure to render tufte_handout Rmarkdown

    - You have sufficient Google BigQuery authentication in the rendering session to succeed with the

buildPancanSE example

        - this would imply that you have a valid project-id for BigQuery; we'll pretend it is "xyz-abc-def"

    - You load MultiAssayExperiment, BiocOncoTK, and then load("blcaMAE.rda")

    - You run the command 

    ```

    assay(experiments(blcaMAE)$meth)@seed@seed@filepath@bqconn@billing = "xyz-abc-def" # USE YOUR CODE

    ```

    - You verify that assay(experiments(blcaMAE)$meth) retrieves some data from BigQuery

    - You save(blcaMAE, file="blcaMAE.rda)

    - render("ccl.Rmd")

- The program panel.R will generate the multiboxplot panel.  It likewise

requires that BiocOncoTK::pancan_BQ(...) succeed meaningfully, either

by picking up a value for CGC_BILLING from the environment, or having

a billing code supplied as `billing` parameter