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. CallsselectMethods()
. -
[()
: 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