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junseonghwan / PhylEx

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Create a separate module for performing copy number inference. #25

Open junseonghwan opened 3 years ago

junseonghwan commented 3 years ago

This is to separate out the CN inference as a post-processing step of PhylEx.

And set up the structure include the main function and parsing of the configuration file.

junseonghwan commented 3 years ago

Read in the config file containing

  1. the path to tree file: just a simple text file with the list of nodes with the name convention from TSSB paper.
  2. assignment of cells to nodes
  3. gexpr matrix for the cells (see #23)

The code may be executed from R, after cleaning up the output from PhylEx.

The code may have some overlap with #22 where we read in a state and continue the MCMC run.