Get cell scores from CoPro object

This function provides a safe way to access cell scores from CoPro objects, using the flat structure for efficient access. It works with both single-slide (CoProSingle) and multi-slide (CoProMulti) objects.

Usage

getCellScores(
  object,
  sigma,
  cellType,
  slide = NULL,
  ccIndex = NULL,
  cells = NULL,
  verbose = TRUE
)

# S4 method for class 'CoProSingle'
getCellScores(
  object,
  sigma,
  cellType,
  slide = NULL,
  ccIndex = NULL,
  cells = NULL,
  verbose = TRUE
)

# S4 method for class 'CoProMulti'
getCellScores(
  object,
  sigma,
  cellType,
  slide = NULL,
  ccIndex = NULL,
  cells = NULL,
  verbose = TRUE
)

Arguments

object

A CoPro object (CoProSingle or CoProMulti)

sigma

Numeric sigma value for which to retrieve cell scores

cellType

Character string specifying the cell type

slide

Character string specifying slide ID (only for CoProMulti objects, ignored for CoProSingle)

ccIndex

Optional integer specifying which canonical component to extract (1-based). If NULL (default), returns the entire matrix

cells

Optional character vector of specific cell IDs to extract. If NULL (default), returns all cells

verbose

Logical indicating whether to print informative messages (default: TRUE)

Value

A matrix of cell scores with cells as rows and canonical components as columns. If ccIndex is specified, returns a vector of scores for that component. If cells is specified, returns only those specific cells.

Details

The function uses a flat structure for efficient access:

• Cell scores are stored with names like "cellScores|sigma0.1|TypeA"

For multi-slide objects, cell scores are aggregated across slides and specific slide filtering is done using the metaDataSub slot.

Examples

if (FALSE) { # \dontrun{
# Get all cell scores for a specific sigma and cell type
scores <- getCellScores(object, sigma = 0.1, cellType = "TypeA")

# Get scores for a specific canonical component
cc1_scores <- getCellScores(object, sigma = 0.1, cellType = "TypeA", ccIndex = 1)

# Get scores for specific cells
specific_scores <- getCellScores(object, sigma = 0.1, cellType = "TypeA", 
                                 cells = c("cell_1", "cell_2"))

# For multi-slide object, specify slide
slide_scores <- getCellScores(object, sigma = 0.1, cellType = "TypeA", 
                              slide = "slide1")
} # }