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morinlab / GAMBLR.results

A collection of functions to access results of the Genomic Analysis of Mature B-cell Lymphomas
MIT License
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Parameter harmonization, prefix cBioPortal functions + removing migrated functions #8

Closed mattssca closed 1 year ago

mattssca commented 1 year ago

This PR addresses a few different things:

  1. Harmonization of the seq type parameter (this_seq_type) so that this parameter is consistent throughout GAMBLR.results and GAMBLR.data.
  2. The plotting function heatmap_mutation_frequency_bin has been removed, since its new home is GAMBLR.viz.
  3. All functions that are associated with cBioPortal functionality have been renamed with the prefix cbio_ to further clarify the intended use of these functions (similarly to functions in the get_ family...).
  4. get_ssm_by_regions has been updated to correctly return n columns based on the parameter usage (https://github.com/morinlab/GAMBLR.results/issues/5)
  5. Package documentation has been updated to reflect these changes.