Hello,

Is there a way to get more information about the paired synteny blocks used to construct the synteny network in syntenet R package? The microsynteny network basically contains the anchor pairs but how do I find which blocks these anchor pairs belong to? I would like to find information on the size of blocks, no of gaps and potentially also on which chromosomes they are.

Thanks

Alex

Hi, Alexandros.

Sorry for the late reply, but there's a bug in the support site (that hasn't been fixed for months already) that makes us not get emails anymore when someone asks a question related to our packages.

Regarding your question, the function infer_syntenet() calls the helper functions intraspecies_synteny() and interspecies_synteny() to detect synteny. These two functions return the path to .collinearity files, the same output of MCScan. By default, these .collinearity go to tempdir(), but you can change that in the argument outdir of infer_syntenet().

Then, you can use the function parse_collinearity() to read these .collinearity files as data frames with the option as = "all". By default, it reads the files with as = "anchors", which means that only the anchor pairs will be included in the data frame. If you want extra information on the anchor pairs, using as = "all" in parse_collinearity() does the job.

I hope it helps,

Best, Fabricio