Create S4 exprObj

Create an exprObj (thin metadata wrapper/adapter) for Giotto expression value information. matrix and tabular formats will be coerced to Matrix sparse format dgCMatrix. For tabular inputs, the first column is used as row names.

Alternative and disk-backed formats

Pre-constructed backed matrices (HDF5Array, dbMatrix, tiledb_array, IterableMatrix) may also be passed directly to expression_data and will be used as-is.

Usage

createExprObj(
  expression_data,
  name = "test",
  spat_unit = "cell",
  feat_type = "rna",
  provenance = NULL,
  misc = NULL,
  expression_matrix_class = deprecated()
)

Arguments

expression_data

expression data. Accepts matrix-like data and coercible data.frame formats (first column used as row names). A filepath to a flat file readable by data.table::fread() can also be passed.

name

name of exprObj

spat_unit

spatial unit (e.g. "cell")

feat_type

feature type (e.g. "rna", "dna", "protein")

provenance

origin data of expression information (if applicable)

misc

misc about the object to attach

expression_matrix_class

deprecated. Previously wrapped the matrix in a DelayedArray when selected. Moving forward, pass a pre-constructed backed matrix to expression_data directly if needed.

Value

exprObj wrapping the expression matrix with spat_unit, feat_type, and provenance metadata attached.

Examples

m <- matrix(rpois(100, 1), nrow = 10,
    dimnames = list(paste0("feat", 1:10), paste0("cell", 1:10))
)
createExprObj(m)
#> An object of class exprObj : "test"
#> spat_unit : "cell"
#> feat_type : "rna"
#> 
#> contains:
#> 10 x 10 sparse Matrix of class "dgCMatrix"
#>                          
#> feat1 . 1 2 3 3 . . . 1 1
#> feat2 2 . 2 1 . 1 1 1 3 1
#> feat3 1 1 . 1 2 2 1 1 2 .
#> feat4 1 2 . 1 . 1 1 2 1 .
#> 
#>  ........suppressing 2 rows 
#>                           
#> feat7  2 1 . 2 . 1 1 1 . 3
#> feat8  2 1 . . . . 1 1 1 .
#> feat9  1 2 2 . . 1 1 1 1 1
#> feat10 3 . 1 . . 4 1 1 2 2
#> 
#>  First four colnames:
#>  cell1 cell2 cell3 cell4 

# example 0-dominated sparse matrix
x_expr <- readRDS(system.file("extdata/toy_matrix.RDS",
    package = "GiottoClass"
))
createExprObj(expression_data = x_expr)
#> An object of class exprObj : "test"
#> spat_unit : "cell"
#> feat_type : "rna"
#> 
#> contains:
#> 10 x 10 sparse Matrix of class "dgCMatrix"
#>                      
#> a . . . . . . . . . .
#> b . . . . 1 . . . . .
#> c . . . . . . 1 . . .
#> d . . . . . . . . . 1
#> 
#>  ........suppressing 2 rows 
#>                      
#> g 1 . . . . . . . . .
#> h 1 . . . . . . . . 1
#> i . . . . . . . . . .
#> j . . . 1 . 1 . . . .
#> 
#>  First four colnames:
#>  A B C D