Get pseudo-bulk coverage files

[Dazcam]

Is there a method to view/manipulate the pseudo-bulk coverage files generated by ArchR within Rstudio? I see that the relevant h5 fragment files are in the Group coverages directory in my ArchR project but I've had a look through the list of Get functions on your reference page and I don't see anything relevant (though I may have missed the function).

Is there an ArchR function/method I could use to access these files within my Rstudio session?

Many Thanks.

[rcorces]

Can you clarify what you mean by pseudo-peak files? Do you mean the pseudo-bulk coverage files or the peak files that result from calling peaks on those pseudo-bulk coverage files? Or something else perhaps?

[Dazcam]

Apologies, I'm referring to the pseudo-bulk coverage files. I've amended the OP.

[rcorces]

Unfortunately, we dont provide any functions to manipulate those coverage files. I think that is the safest implementation to prevent end users from messing with a file that is important for downstream analysis.
Have you looked at the getGroupBW() function? This exports a bigWig file that is similar (though not the same replicates etc) as the coverage files and you could edit that.
https://www.archrproject.com/reference/getGroupBW.html

If you have a particular application in mind, feel free to let us know and we will assess whether it makes sense to implement.

[Dazcam]

No problem. Thank you for responding. I suspected that might be the case. I was looking to export the files (in some way) to run on a different peak caller. I can see you have a function for converting the coverage files to bed files in preparation for peak calling in macs2. Are these coverage bed files stored anywhere?

[rcorces]

The bed files are generated and then removed automatically in the .callSummitsOnCoverages() hidden function via the .writeCoverageToBed() hidden function.

You should be able to use this function via ArchR:::.writeCoverageToBed() to generate the bed files you want

ArchR/R/GroupCoverages.R

Line 739 in 968e442

.writeCoverageToBed <- function(coverageFile = NULL, out = NULL, excludeChr = NULL, logFile = NULL){