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Clone- and haplotype specific cancer karyotypes inferred with RCK on 17 prostate cancer samples
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README.md

README.md

Clone- and haplotype specific cancer karyotypes inferred with RCK (paper|code) on 17 prostate cancer samples

Directories are organized as follows:

  sample/cna/sample_cna-fp.rck.(a|s)cnt.tsv

where:

  • sample -- sample identifyer (e.g., A10c, where A10 is the patient id in the original paper (link) and c is the sample from the respective patient).
  • cna -- input allele-specific segment copy number tensor from either Battenberg or HATCHet.
  • fp -- False Positive paramter for the input Novel Adjacenceis utilization (i.e., reconstrcuted keryotypes must have at least 1-fp fraction of input Novel Adjacencies being present across all the clones in the sample)

acnt determines the adjacency copy number tensor, with copy numbers for every input novel adjacency (labeled versions) in every clone, as well as for every reference adjacency.

scnt determines the segment copy number tensor with clone- and haplotype-specific copy numbers.

For more information on both segment and adjacency copy number tensors formats, please, refer to the original RCK repository "results" section.

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