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Wedge-lab / dpclust

Dirichlet Process based methods for subclonal reconstruction of tumours
GNU Affero General Public License v3.0
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Error in dpclust3p #11

Closed gevro closed 3 years ago

gevro commented 3 years ago

Hi, I'm getting this error when running dpclust3p:

Error in data.frame(as.character(seqnames(v)), start(ranges(v)), counts_table,  : 
  arguments imply differing number of rows: 5420, 0
Calls: dumpCounts.Sanger -> dumpCountsFromVcf -> formatOutput -> data.frame

I think I've traced the bug to this function: dpclust3p:::getCountsTumour. This function is called by dpclust3p:::dumpCountsFromVcf, which in turn is called by dumpCounts.Sanger, in the the example pipeline you give in https://github.com/Wedge-lab/dpclust3p/blob/master/inst/example/preproc_pipeline_caveman.R.

However, your pipeline does not provide any way to change the value of the 'centre' variable which is first used by dumpCountsFromVcf.

Without being able to configure the 'centre' variable in your dpclust3p pipeline, dpclust3p doesn't work. Instead it defaults to centre = 'sanger', which means that this pipeline is only usable by data produced by Sanger pipeline.

Note a similar issue is that refence_genome = "hg19" as default in dumpCountsFromVcf, and dumpCounts.Sanger also does not allow changing that default, which means that the dpclust3p example pipelines do not allow setting to the correct reference genome.

Do you have a pipeline that would allow using dpclust on data that was produced outside of sanger?

Thanks!

gevro commented 3 years ago

Hi, I see that the solution is to use dumpCountsFromVcf instead of dumpCounts.Sanger.

I think it might help to have an example pipeline that uses dumpCountsFromVcf, since that is what people with data outside of sanger would need in order to run dpclust.

gevro commented 3 years ago

Just use dumpCountsFromVcf instead of dumpCounts.Sanger. If you search for that function in the code, you can see the details of how it works.

gevro commented 3 years ago

I don't remember that happening, but I think you can try to find the function in the source code and just load it manually.

shaghayeghsoudi commented 3 years ago

thank you , yup just digging in to codes now

gevro commented 3 years ago

I'm sorry I don't remember what I did actually to fix it. Can you give me your e-mail address to connect directly offline?