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smgogarten / GWASTools

Classes for storing very large GWAS data sets and annotation, and functions for GWAS data cleaning and analysis
https://bioconductor.org/packages/GWASTools
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Request to Replace Sweave Vignettes with R Markdown #13

Open sonali8434 opened 1 year ago

sonali8434 commented 1 year ago

Hello @smgogarten, I'm a Sweave2Rmd volunteer. @jwokaty and I are trying to replace Bioconductor Sweave vignettes with R Markdown. It has many advantages over Sweave vignettes, such as R Markdown converts to HTML, uses BiocStyle, and is easier to maintain.

Would you consider accepting pull requests for R Markdown versions of the following vignettes from one of our volunteers?

We'll ask you to review and accept the pull request. You'll also need to bump the version number in your DESCRIPTION file so that the Bioconductor build machines will recognize that a new version is available.

Thank you for your time, I look forward to your response.

smgogarten commented 1 year ago

Yes, absolutely! Thank you for doing this!

sonali8434 commented 1 year ago

Thank you!

sonali8434 commented 1 year ago

Hello, @smgogarten!

I wanted to inform you that I have submitted a pull request for the conversion of GWASTools/vignettes/Affymetrix.Rnw. Kindly take a look at it when you have some free time.

Thank you for your valuable time!

jwokaty commented 1 year ago

Hi @smgogarten

I work with Somali on Sweave2Rmd. I noticed that in DataCleaning.Rnw the URLs for the Geneva project at http://www.genevastudy.org/ and Genomic Data Structure at http://corearray.sourceforge.net/ are out of date. I know that information can get out of date so before we perform any further work, I want to ask if DataCleaning.Rnw is still a viable vignette and these URLs or this section should be updated? Or do you plan to deprecate this vignette in the future such that it should not be converted? I would appreciate your guidance. Thanks for working with us!

Jen

smgogarten commented 1 year ago

The vignette is still viable; when you do the Rmd conversion could you please update the URLs as follows: http://www.genevastudy.org/ -> https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2860056/ http://corearray.sourceforge.net/ -> https://github.com/zhengxwen/gdsfmt Thank you!