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robinweide / GENOVA

GENome Organisation Visual Analytics
GNU General Public License v3.0
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CSCAn -> visualise error #297

Closed odovgusha closed 1 year ago

odovgusha commented 2 years ago

Describe the bug After running test = GENOVA::CSCAn(synched, bedlist = list(diff_atac_df[1:500,],all_ATAC_peaks[1:500,]))

I get Error in rep(5.5, length(unique(df$right)) - 1L) : invalid 'times' argument

after running visualise(test)

Also, just wanted to ask a question about CScan function because I am a bit confused. PE-scan aggregates all interaction signals between a set of regions. For C-scan you need to provide at least 2 sets of regions. Doest it aggregates all the signals between two groups. i.e I have 5 promoters and 5 enhancers. Will C-scan look for the interaction signal of each promoter vs all the enhancers and then sum all the interactions of these promoters with enhancers?

Many thanks!

teunbrand commented 2 years ago

Thanks for reporting! I can indeed confirm that this error is thrown when 2 sets of regions are provided. Hoping to get a fix in soon.

C-Scan indeed looks for all locations where sets of regions might interact, within some distance (by default, a minimum of 50kb and maximum of 2Mb), and then aggregates this per set combination. It does not look for within-set interactions, that is what PE-Scan does.

teunbrand commented 2 years ago

Should be fixed now on dev branch :)

odovgusha commented 2 years ago

Many thanks! Sorry, could you suggest how to install the GENOVA from dev branch?

teunbrand commented 2 years ago

Sure, typically you can install from the dev branch in the following manner:

devtools::install_github("robinweide/GENOVA", ref = "dev")