Function to create a new object

Function to create a new object

Usage

newCoProSingle(normalizedData, locationData, metaData, cellTypes)

# S4 method for class 'ANY,matrixOrDataFrame,data.frame,factorOrCharacter'
newCoProSingle(normalizedData, locationData, metaData, cellTypes)

Arguments

normalizedData

A matrix object to store normalized data.

locationData

A data.frame object to store the location. It should either contain two columns named by "x" and "y", or three columns named by "x", "y", and "z". No other names allowed

metaData

A data.frame object to store metadata for each cell.

cellTypes

A vector object with elements being character. It should match the number of cells in the data matrix and each represents a cell type label of a cell.

Value

A CoPro object

See also

newCoProMulti(), CreateCoPro(), asCoProSingle()

Other object-creation: asCoPro, newCoProMulti(), subsetData()

Examples

toy <- readRDS(system.file("extdata", "toy_copro_data.rds", package = "CoPro"))
obj <- newCoProSingle(
  normalizedData = toy$normalizedData,
  locationData   = toy$locationData,
  metaData       = toy$metaData,
  cellTypes      = toy$cellTypes
)
obj
#> 'CoProSingle' object for spatial coordinated progression detection
#> ------------------------
#> Number of cells: 200
#> Number of genes: 80
#> Number of slides: 1 (single-slide analysis)
#> 
#> Processing steps completed:
#> 
#> Available metadata fields:
#> - cell_id
#> - cell_type
#> 
#> Approx. object size: 0.20 MB