In GenomicInteractions v.1.10.0, the plotCisTrans function uses the is.cis and is.trans functions to note the number of cis and trans interactions respectively.

cis_p <- sum(is.cis(GIObject))
trans_p <- sum(is.trans(GIObject))

Due to the logical return value of is.cis and is.trans, isn't this actually reporting just the number of cells in the contact matrix (or the number of interactions in the GIObject) that correspond to cis and trans interacting loci respectively? For a given resolution, this will only change when only the non-zero cells of the contact matrix are reported/stored (sparse format) in the GIObject.

I am wondering, is this what it is intended to do?

Because, given the description of plotCisTrans function in the vignette/help, I would expect it to report the percentages of  cis-interaction counts and trans-interaction counts in the contact matrix or the GIObject, because that seems to be the more interesting thing in general. But, I may have misunderstood. I know that this can be easily achieved using the sum function as follows:

sum(GIObject[ which(is.cis(GIObject) == TRUE), ])

Just making sure that this is not erroneously so.

Thank you very much.

Best,

Sarvesh

Hi Sarvesh, you are correct - this is reporting the number of non-zero cells, and that's what it's intended to do. I guess the terminology of interactions and interaction counts can be confusing, sorry about that. Do you think the documentation needs changing? We tried to be consistent with the terms but might have slipped up.

Hi Malcolm, thanks for the reply and clearing the confusion for me. May be it could be made clear in the documentation.

In case it helps, what confused me is that, for a genome-wide Hi-C contact matrix that I read in as a GIObject, the percentage of cis-interactions was less than the trans-interactions in the plot, contrary to what I knew about my contact matrix. Only after looking at the code I realized that this is due to the fact that the non-zero cells are being reported.

Thanks again.

And, great work with the package!