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Release v1.2.0
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@ShixiangWang ShixiangWang released this 06 Jan 06:45
· 280 commits to master since this release
v1.2.0
4d042cd

BUG REPORTS

ENHANCEMENTS

  • A new option cut_p_value is added to show_group_enrichment() to cut continous p values as binned regions.
  • A Python backend for sig_extract() is provided.
  • User now can directly use sig_extract() and sig_auto_extract() instead of loading NMF package firstly.
  • Added benchmark results for different extraction approaches in README.
  • The threshold for auto_reduce in sig_fit() is modified from 0.99 to 0.95 and similarity update threshold updated from >0 to >=0.01.
  • Removed pConstant option from sig_extract() and sig_estimate(). Now a
    auto-check function is created for avoiding the error from NMF package due to
    no contribution of a component in all samples.

NEW FUNCTIONS

  • bp_show_survey2() to plot a simplified version for signature number survey (#330).
  • read_xena_variants() to read variant data from UCSC Xena as a MAF object for signature analysis.
  • get_sig_rec_similarity() for getting reconstructed profile similarity for Signature object (#293).
  • Added functions start with bp_ which are combined to provide a best practice for extracting
    signatures in cancer researches. See more details, run ?bp in your R console.

DEPRECATED

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