TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages (workflow package)

tiagochst commented 7 years ago

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tiagochst commented 7 years ago

I just found . Sorry

bioc-issue-bot commented 7 years ago

Hi @tiagochst,

Starting build on additional package https://github.com/BioinformaticsFMRP/TCGAWorkflowExampleData.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your additional package repository will NOT trigger a new build.

The DESCRIPTION file of this additional package is:

Package: TCGAWorkflowExampleData
Title: Example data for TCGA Workflow 
Version: 0.99.0
Date: 2017-01-31
Author: Tiago Chedraoui Silva  <tiagochst@usp.br>
Maintainer: Tiago Chedraoui Silva <tiagochst@usp.br>
Description: An small dataset that can be used to run examples from the TCGAWorkflow vignette
Depends:
R (>= 3.4.0)
Imports: SummarizedExperiment
License: GPL-3
VignetteBuilder: knitr
biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData
NeedsCompilation: no
URL: https://f1000research.com/articles/5-1542/v2
BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues
RoxygenNote: 5.0.1
Suggests: 
knitr,
rmarkdown,
pander

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

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bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

9165c54 Fixing example

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676376a Removing warnings

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bioc-issue-bot commented 7 years ago

Received a valid push; starting a build. Commits are:

e87a126 Adding mutation data into the experimental package

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vobencha commented 7 years ago

Review of data package:

Change name to TCGAWorkflowData
In the Description field of the DESCRIPTION file please say what kind of data these are, e.g., 9 data sets of expression data for cancer XYZ for 100 samples from https://download/site etc.
Remove 'Date' field from DESCRIPTION; this will be auto generated when the package is built with R CMD build
The man pages can be separate or all on one page. A single page would probably be more efficient here because all man pages must have i) more detail about how the data were processed, how the subsets were made etc. ii) an \example section that shows how to load the data (if only one man page you only need to show how to load a couple of datasets) iii) define abbreviations such as GBM (what does this mean?)

Here is an example of a complete man page for a data set:

> library(pasillaBamSubset)
> ?pasillaBamSubset

Note how the name of the data package brings you to one page that lists all data sets - very easy to find.

Valerie

vobencha commented 7 years ago

You've done a great job with the vignette in the data package. You could reference users to that on the man page(s) with browseVignettes("TCGAWorkflowData"). The man pages still need a mention of what I outlined above but the bulk of the detail re: creating the datasets can be in the vignette.

tiagochst commented 7 years ago

AdditionalPackage: https://github.com/BioinformaticsFMRP/TCGAWorkflowData

bioc-issue-bot commented 7 years ago

Hi @tiagochst,

Starting build on additional package https://github.com/BioinformaticsFMRP/TCGAWorkflowData.

IMPORTANT: Please read the instructions for setting up a push hook on your repository, or further changes to your additional package repository will NOT trigger a new build.

The DESCRIPTION file of this additional package is:

Package: TCGAWorkflowData
Title: Data for TCGA Workflow 
Version: 0.99.3
Author: Tiago Chedraoui Silva  <tiagochst@usp.br>
Maintainer: Tiago Chedraoui Silva <tiagochst@usp.br>
Description: 
  This experimental data package has the data necessary to follow the 
  TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages.
  It contains the following files:
- GBMnocnvhg19: segmented CNV from SNP array (Affymetrix Genome-Wide Human SNP Array
  6.0) for 20  Glioblastoma multiforme (GBM)  samples.
   - GBMIllumina_HiSeq: a matrix with  raw expression signal for expression of a gene for
 20 GBM (Glioblastoma multiforme) samples
   - LGGIllumina_HiSeq: a matrix with  raw expression signal for expression of a gene for
 20 LGG (Lower grade glioma) samples
   - met.20.samples.GBM.LGG.chr9:  DNA methylation matrix from Infinium HumanMethylation450 platform 
 for 10 LGG (Lower grade glioma) and 10 GBM (Glioblastoma multiforme). 
 It has only probes in chromossome 9  in order to make the example  of the workflow faster
   - elmer.example: Contains a DNA methylation matrix (only probes in chromossome 9) and a gene expression matrix for 
 10  LGG (Lower grade glioma) and 10 GBM (Glioblastoma multiforme) in the required format
 for to execute the R/Bioconductor ELMER package analysis and a vector 
 identifying which sample belongs to each tumor type.
   - maf_mutect2_LGG_GBM: Mutation annotation files for LGG (Lower grade glioma) and GBM (Glioblastoma multiforme)
 samples merged into a single matrix. The GDC Somatic Mutation Calling Workflow mutect2 was used to create this MAF files. 
   - markersMatrix: Probes meta file from broadinstitute website for Copy Number Variation Analysis (CNV) analysis
  For more information how to create these objects please read the vignette of this package 
  (You can open it with browseVignettes("TCGAWorkflowData")))
Depends:
R (>= 3.4.0)
Imports: SummarizedExperiment
License: GPL-3
VignetteBuilder: knitr
biocViews: ExperimentData, Homo_sapiens_Data, MicroarrayData
NeedsCompilation: no
URL: https://f1000research.com/articles/5-1542/v2
BugReports: https://github.com/BioinformaticsFMRP/TCGAWorkflow/issues
RoxygenNote: 5.0.1
Suggests: 
knitr,
rmarkdown,
pander

bioc-issue-bot commented 7 years ago

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bioc-issue-bot commented 7 years ago

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eaf36bf Fixing experimental data package

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tiagochst commented 7 years ago

Hi @vobencha, just one question. The workflows accepts any type of Rmd? I was thinking to update it to use DT package to shows some tables. Like here: http://bioinformaticsfmrp.github.io/TCGAbiolinks/query.html

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68fd983 Fixing RTCGAtoolbox part as pointed by reviewer.

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vobencha commented 7 years ago

Not sure where we are on this. When you're ready for me to take another look mention me @vobencha. Valerie

tiagochst commented 7 years ago

Hi, sure. I'm working on other projects right now. I should be back on this next week. Once I fix the problems I'll mention you. I have just one question. One of the problems is timeout ( TIMEOUT: R CMD build exceeded 10mins). This limit is new for workflows?

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Bioconductor / Contributions

TCGA Workflow: Analyze cancer genomics and epigenomics data using Bioconductor packages (workflow package) #229