How do I point to files?

[f6v]

Hi!

Thanks for the package! I can't figure out how to point to the files though. I've ran nf-core/methylseq pipeline and that outputs coverage2cytosine Bismark results like these:

Here's how sample_info.xlsx looks like:

I change the working directory of the R session to folder with these files and run:
DM.R(genome = "mm10", testCovariate = "Age", cores = 8)
However, there's an error:

[DMRichR] Processing Bismark cytosine reports            19-09-2023 09:23:47 PM
Selecting files... 
Reading cytosine reports...    
Error in bsseq::read.bismark(files = files, rmZeroCov = FALSE, strandCollapse = TRUE,  : 
These files cannot be found: 
NA

What am I missing?

[f6v]

I guess the issue is that running https://github.com/ben-laufer/DMRichR/blob/0b6176a1be386b839f0f6def51fa7226310d2ad6/R/processBismark.R#L44C40-L44C40 returns NA for Treg9 sample. Any idea how to fix that?

[f6v]

Ok so I debugged it for a while, and I guess the issue is that the tool makes an assumption that file name has an underscore before the sample name. I made it work by changing the file names and sample names in the excel sheet.