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FunGeST / Palimpsest

An R package for studying mutational signatures and structural variant signatures along clonal evolution in cancer.
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Error running deconvolution_fit_SV with plotting #59

Open anoronh4 opened 2 years ago

anoronh4 commented 2 years ago

Using the example script with the example Rdata gives me the following error:

Error in RCircos.Validate.Genomic.Data(genomic.data, "link", genomic.columns) : 
  One or more genomic position in plot data is
outside of chromosome length for chr4.
Calls: deconvolution_fit_SV ... RCircos.Get.Paired.Points.Positions -> RCircos.Validate.Genomic.Data
edceeyuchen commented 2 years ago

I have the same problem! Could you solve it? Thanks!

jpmcelderry commented 1 year ago

For anyone with this problem in the future, deconvolution_fit_SV has an argument gv, or 'genome version'. This is set to "hg38" default, and needs to be manually set for the script to "hg19" instead.

edceeyuchen commented 1 year ago

@jpmcelderry Hello! Sorry for lately reply, I want to know, if I used my SV data, there is no need to change the 'genome version', right? Hope your help~

jpmcelderry commented 1 year ago

@jpmcelderry Hello! Sorry for lately reply, I want to know, if I used my SV data, there is no need to change the 'genome version', right? Hope your help~

I imagine it just depends on your SV data genome version. If your SV data is in hg38 coordinates then this matches the default value of gv. If your data is in hg19 coordinates you will need to set gv="hg19".

edceeyuchen commented 1 year ago

@jpmcelderry Hello! Sorry for lately reply, I want to know, if I used my SV data, there is no need to change the 'genome version', right? Hope your help~

I imagi ne it just depends on your SV data genome version. If your SV data is in hg38 coordinates then this matches the default value of gv. If your data is in hg19 coordinates you will need to set gv="hg19".

Thank you! And totally I understand now~