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RabadanLab / arcasHLA

Fast and accurate in silico inference of HLA genotypes from RNA-seq
GNU General Public License v3.0
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Interpretation of HLA LOH results #82

Open eseffar opened 2 years ago

eseffar commented 2 years ago

Hi, First at all, thank you for this wonderful tool. I have some questions about the files generated by quant function of arcasHLA.

I'm wondering what does significate the results in the quant.loh.tsv file. Here the result file I'm currently working on : image

Of course it seems some alleles are loss for this tumor sample but what does number means ? Is this expression ? CN means CopyNumber ?

How can I use the results files to visualize HLA LOH ? Compare TPM values for each allleles from quant.allleles.tsv file or the values in quant.loh.tsv ?

I would like to create plots like this one : image

Thank you in advance for your answer.

Evan

naity2 commented 2 years ago

Hi @Evan-SF, I was wondering if you made any process on this? Thanks!

Portulaca666 commented 8 months ago

Hi , I was also wondering if you made any process on this? Thanks!