olli0601 / phyloscanner.r.utilities Goto Github PK

Hi Oliver,

I noted that the count.pairwise.relationships() and classify.pairwise.relationships() functions for reconstructing transmission networks have now been integrated into the latest phyloscannerR release (v1.8.0) and was wondering whether there any plans to integrate the phsc.find.transmission.networks.from.linked.pairs() and phsc.plot.most.likely.transmission.chain() functions as well?

I am asking as the data frames output by count.pairwise.relationships() and classify.pairwise.relationships() in phyloscannerR (v1.8.0) are currently different from the input expected by phsc.find.transmission.networks.from.linked.pairs() and phsc.plot.most.likely.transmission.chain() in Phyloscanner.R.utilities

Thanks,

Hello
I tried to apply your nice tutorial to my data.
I started creating the bash scripts using the same parameters with 6 bam files and their own reference.
everything goes well for crating the pty.runs but I have the following error when running

pty.c <- phsc.cmd.phyloscanner.multi(pty.runs, pty.args)

The following objects are masked from pty.args (pos = 11):

    alignments.file, alignments.pairwise.to, alignments.root, all.bootstrap.trees, data.dir, dont.check.duplicates, dont.check.recombination, keep.overhangs, mem.save,
    merge.paired.reads, merge.threshold, min.internal.quality, min.read.count, no.trees, num.bootstraps, out.dir, prog.mafft, prog.pty, quality.trim.ends, select, verbose,
    win, window.automatic, work.dir

Error in phsc.cmd.phyloscanner.one(pty.args, file.input, file.patient) : 
  object 'default.coord' not found

anything I am missing?