Apply a function to every element of a bumpy matrix. — apply_bumpy

Apply a user-specified function to every element of a bumpy matrix.

Usage

apply_bumpy_function(
  se,
  FUN,
  req_assay_name,
  out_assay_name,
  parallelize = FALSE,
  ...
)

Arguments

se: A SummarizedExperiment object with bumpy matrices.
FUN: A function that will be applied to each element of the matrix in assay req_assay_name. Output of the function must return a data.table.
req_assay_name: String of the assay name in the se that the FUN will act on.
out_assay_name: String of the assay name that will contain the results of the applied function.
parallelize: Logical indicating whether or not to parallelize the computation.
...: Additional args to be passed to teh FUN.

Value

The original se object with a new assay, out_assay_name.

Examples

mae <- get_synthetic_data("finalMAE_small.qs")
se <- mae[[1]]
FUN <- function(x) {
  data.table::data.table(Concentration = x$Concentration, CorrectedReadout = x$CorrectedReadout)
} 
apply_bumpy_function(
  se, 
  FUN = FUN, 
  req_assay_name = "RawTreated", 
  out_assay_name = "CorrectedReadout"
)
#> class: SummarizedExperiment 
#> dim: 10 10 
#> metadata(5): identifiers experiment_metadata Keys fit_parameters
#>   .internal
#> assays(6): RawTreated Controls ... Metrics CorrectedReadout
#> rownames(10): G00002_drug_002_moa_A_72 G00003_drug_003_moa_A_72 ...
#>   G00010_drug_010_moa_A_72 G00011_drug_011_moa_B_72
#> rowData names(4): Gnumber DrugName drug_moa Duration
#> colnames(10): CL00011_cellline_BA_tissue_x_26
#>   CL00012_cellline_CA_tissue_x_30 ... CL00019_cellline_JB_tissue_z_58
#>   CL00020_cellline_KB_tissue_z_62
#> colData names(4): clid CellLineName Tissue ReferenceDivisionTime