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waldronlab / cBioPortalData

Integrate the cancer genomics portal, cBioPortal, using MultiAssayExperiment
https://waldronlab.io/cBioPortalData/
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Update and rename cgdsMigration.Rmd to cgdsrMigration.Rmd #53

Closed kmezhoud closed 2 years ago

kmezhoud commented 2 years ago

get Studies, Cases/Samples, Clinical Data, mRNA, mutations, endpoints

LiNk-NY commented 2 years ago

Hi Karim, @kmezhoud It is hard to compare the differences between the files. I will rename first to see if that helps.

kmezhoud commented 2 years ago

Hi Marcel, @LiNk-NY Sure! It will easiest to run the .Rmd file locally and show the html output. GitHub cannot do that for us. Karim

LiNk-NY commented 2 years ago

Hi Karim, @kmezhoud Can you merge the devel branch into yours?

kmezhoud commented 2 years ago

Hi Marcel, @LiNk-NY , I will do that. But I will have the same 9 conflicts, which are the Mains differences between files. To solve the conflicts, just delete/remove one PART of two choices. 

<<<<<<<<branch1
PART 1:  SUGGESTED/NEW VERSION
=============
PART 2:  ACTUAL/OLD VERSION
>>>>>>>>branch2

Example of the title conflict:

<<<<<<< devel
title: "Migrating from cgdsr to cBioPortalData"
=======
title: "cgdsr Migration"
>>>>>>> devel

To resolve this conflict just leave the desired title and delete the rest. During resolving conflict you will be able to compare the difference between files.

Karim

LiNk-NY commented 2 years ago

Hi Karim, @kmezhoud

It may be easier to create a new branch based on the devel branch and add copy and paste your changes to the vignette. The multiple renames threw off the git diff print out that you could have saved (rather than copying an pasting). It would then be easier to see the differences in the vignette after you create a new pull request. Thank you!

Best, Marcel