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sartorlab / mint

A pipeline for the integration of DNA methylation and hydroxymethylation data
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How can I obtain the table of complete annotations described in the README.md file? #27

Open mdperry opened 3 years ago

mdperry commented 3 years ago

Hi, I have been able to install and run this version of mint on both my BioLinux laptop running Ubuntu 14.04 as well as an HPC running CentOS; in both cases using your test_hybrid_small demo dataset. Now I am trying to get all of the makefile modules to run on real live patient data from our article published in Nature Genetics in AUG-2020. It would potentially be quite useful if there was a simple way to create the "Table: complete annotations" that is shown in the GitHub documentation, the relevant text says, "All annotation sessions output a table of all genomic annotations intersecting the input regions in test_hybrid_small/summary/tables." Thus far I have not been able to find this table, just the _annotation_counts.txt tables and the _annotation_counts_by_category.txt tables. I have searched through all of the mint code, as well as in the annotatr package code, and could not find how this is supposed to be generated. Is this particular feature still supported? Thanks, -- Marc

mdperry commented 3 years ago

Okay, in the interim I have now figured out how to do this by playing around on the R interpreter command line, and loading up one of the annotatr .RData files. So I will add the necessary commands as needed to the annotatr_annotations.R script in mint.

rcavalcante commented 3 years ago

Hi Marc,

Thanks for your interest in mint, and apologies for the delay in response. You are correct, I cannot find a tabular output of the annotations themselves either, and you are correct to look for them in the RData object. In retrospect, I think the output of the annotation table was dropped in favor of dealing with it in R. This particular project is a little cold in my working memory, but for certain assays (WGBS, for example), the table could be prohibitively large to look at reasonably outside of R (in Excel, for example). So in this case, I think the documentation should be updated to reflect that.

Once you're in R and you have the table handy, you could use the readr::write_tsv() function to write all, or a subset, of the results to file. It sounds like you might have already done this.

Again, thanks for your interest in mint, and please follow up with any other issues you might have.

Raymond