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vplagnol / ExomeDepth

ExomeDepth R package for the detection of copy number variants in exomes and gene panels using high throughput DNA sequencing data.
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Documentation #57

Closed pd3 closed 1 year ago

pd3 commented 1 year ago

I'd like to try ExomeDepth because it came out favourable in comparison of other CNV callers https://www.nature.com/articles/s41598-021-93878-2

I installed the package using 

if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
BiocManager::install("ExomeDepth")

and now I am trying to understand how to run it. Is there a document that describes best practices, or any documentation showing how to actually run it?

vplagnol commented 1 year ago

I am hoping that the vignette tells you everything you need to know? You should be able to access it from CRAN or the installed package itself.

pd3 commented 1 year ago

Uh, this seems to assume a background knowledge which I don't have. I am not familiar with .Rnw files and would not guess a file named vignette.Rnw contains the documentation!

Perhaps creating a txt / pdf / html file in a subdirectory labeled 'doc' or 'documentation' would help users like me :)

Thank you for the prompt response.

vplagnol commented 1 year ago

It's the pdf version of the vignette that you want. See this link: https://cran.r-project.org/web/packages/ExomeDepth/vignettes/ExomeDepth-vignette.pdf

vplagnol commented 1 year ago

And to be 100% clear because you may not have worked with these features before, but the magic of R is to create the pdf version of the vignette directly from the markdown Rnw file, so that you can see exactly what is going on.