S4 Interface for SCONE

[mbcole]

Slots

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

Methods

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

[drisso]

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

[drisso]

Commits 4b6fc70aa095e31e5ae290ce53eaa0bfeb84646a..d7db5273802514f454a4abd88d55eb7c2e026614