YosefLab/scone

S4 Interface for SCONE

Closed this issue · 2 comments

mbcole commented

Slots

  • Original Matrix
  • QC Matrix
  • Bio
  • Batch
  • Positive Controls
  • Negative Controls 1
  • Negative Controls 2
  • List of Normalized Matrices
  • File pointer to hdf5 (Alternative)
  • List of Design Matrices (Depend on Bio and/or Batch)
  • List of List of Functions (Impute and Scale)
  • Additional Params or Flags or Arguments (e.g. rezero? and Impute_Args)
  • Metrics
  • Scores
  • Params

Methods

  • get_normalized(): Returns expression matrix for normalized matrix requested (index of params)
  • biplot_interactive(): Interactive bi-plot returns smaller SCONE object based on user selection. Calls selectMethods().
  • [(): Accessing subsets of cells or genes.
  • select_methods(): Accessing subsets of normalizations - look at summarized experiment.
  • get_design(): Returns design matrix.
  • init_report(): Initialize all information required for generating interactive report.
  • report(): View report.
  • write_report(): Produce static report.
  • scone(): Run all normalizations (store hdf5, in_memory, or not) and score.
drisso commented

Add a method for extracting and replacing scone_params: get_params and set_params

drisso commented

Commits 4b6fc70..d7db527