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BioinformaticsFMRP / TCGAWorkflow

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages
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Please update the contents in Bioconductor Workflows section #2

Open mckf111 opened 6 years ago

mckf111 commented 6 years ago

Hi,

I found the example code in the website is sometimes tricky to run (e.g. the code in Visualizing multiple genomic alteration events section, see below), what's more, in the beginning, the workflowInstall can't work, I think it is something related with the bioconductor version. 

...
mut <- mut[mut$Hugo_Symbol %in% Glioma_signaling_genes,]
clinical <- plyr::rbind.fill(gbm_clin,lgg_clin)
...

I found nowhere that the authors declared the 2 variables: gbm_clin, lgg_clin. And there are several more...alas...

So please try to invest a little more time to fix those seeming tiny problems that could really block the workflow from time to time. I think that is a good way to prove to the other researchers this is a truly valuable and applicable workflow.

Sincerely,

Wenhu

tiagochst commented 6 years ago

Hello,

I'll try to update the workflow. Now some packages like ELMER and maftools will need . updates in the code for sure.

gbm_clin and lgg_clin are created in the chunk starting at line 453:

https://github.com/BioinformaticsFMRP/TCGAWorkflow/commit/8048367e47b10f0f535f0eee5201c9a90df0dcbb#diff-2681358fc0c52be9a5a12f5e2ede5311L453

Best regards, Tiago