FilterCCI: Filter a scDiffCom object with new filtering parameters

Description

Filtering (and ORA) is performed with new parameter on an existing scDiffCom object. The slots cci_table_detected and ora_table are updated accordingly.

Usage

FilterCCI(
  object,
  new_threshold_quantile_score = NULL,
  new_threshold_p_value_specificity = NULL,
  new_threshold_p_value_de = NULL,
  new_threshold_logfc = NULL,
  skip_ora = FALSE,
  extra_annotations = NULL,
  verbose = TRUE
)
# S4 method for scDiffCom
FilterCCI(
  object,
  new_threshold_quantile_score = NULL,
  new_threshold_p_value_specificity = NULL,
  new_threshold_p_value_de = NULL,
  new_threshold_logfc = NULL,
  skip_ora = FALSE,
  extra_annotations = NULL,
  verbose = TRUE
)

Value

A scDiffCom object with updated results in cci_table_detected

and ora_table.

Arguments

object: scDiffCom object
new_threshold_quantile_score: New threshold value to update threshold_quantile_score. If NULL (default), the value is not updated.
new_threshold_p_value_specificity: New threshold value to update threshold_p_value_specificity. If NULL (default), the value is not updated.
new_threshold_p_value_de: New threshold value to update threshold_p_value_de. If NULL (default), the value is not updated.
new_threshold_logfc: New threshold value to update threshold_logfc. If NULL (default), the value is not updated.
skip_ora: Default is FALSE. If TRUE, ORA is not performed with the new parameters and ora_table is set to an empty list. May be useful if one wants to quickly test (loop-over) several values of parameters and by-pass the ORA computing time.
extra_annotations: Convenience parameter to perform ORA on user-defined non-standard categories. If NULL (default), ORA is performed on standard categories. Otherwise it must be a list of data.tables or data.frames (see Details).
verbose: If TRUE (default) progress messages are printed.

Details

When FilterCCI is called with new parameters, both cci_table_detected and ora_table are updated. For ORA, a call to RunORA is automatically performed on all standard categories. Additional user-defined ORA categories can be added via the parameter extra_annotations. The data.frames or data.tables in this list must have exactly two columns that indicates a relationship between values from a standard category (first column) to values of the new category (second column). As a typical example, this vignette shows how to perform ORA on cell type families attached to each cell type.