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Aggregate a BumpyMatrix assay by a given aggregation function.

Source: R/concatentate_SEs.R
aggregate_assay.Rd

Aggregation can only be performed on nested variables.

Usage

aggregate_assay(asy, by, FUN)

Arguments

asy

A BumpyMatrix object.

by

Character vector of the nested fields to aggregate by.

FUN

A function to use to aggregate the data.

Value

A BumpyMatrix object aggregated by FUN.

Examples

mae <- get_synthetic_data("finalMAE_small") 
se <- mae[[1]]
assay <- SummarizedExperiment::assay(se)
#> Loading required package: BumpyMatrix
aggregate_assay(assay, FUN = mean, by = c("Barcode"))
#> 10 x 10 BumpyDataFrameMatrix
#> rownames: G00002_drug_002_moa_A_72 G00003_drug_003_moa_A_72 ... G00010_drug_010_moa_A_72 G00011_drug_011_moa_B_72 
#> colnames: CL00011_cellline_BA_tissue_x_26 CL00012_cellline_CA_tissue_x_30 ... CL00019_cellline_JB_tissue_z_58 CL00020_cellline_KB_tissue_z_62 
#> preview [1,1]:
#>   DataFrame with 3 rows and 7 columns
#>         Barcode Concentration ReadoutValue BackgroundValue record_id    masked
#>     <character>     <numeric>    <numeric>       <numeric> <numeric> <numeric>
#>   1     plate_1       1.62492      46.0333               0      1801         0
#>   2     plate_2       1.62492      46.4111               0      1901         0
#>   3     plate_3       1.62492      47.0778               0      2001         0
#>     CorrectedReadout
#>            <numeric>
#>   1          46.0333
#>   2          46.4111
#>   3          47.0778