Merge assay data
Arguments
- SElist
named list of Summarized Experiments
- assay_name
name of the assay that should be extracted and merged
- additional_col_name
string of column name that will be added to assay data for the distinction of possible duplicated metrics that can arise from multiple projects
- discard_keys
character vector of string that will be discarded during creating BumpyMatrix object
Examples
mae <- get_synthetic_data("finalMAE_combo_2dose_nonoise.qs2")
listSE <- list(
combo1 = mae[[1]],
sa = mae[[2]]
)
merge_assay(listSE, "Normalized")
#> $DT
#> data_source Concentration Concentration_2 normalization_type x
#> <char> <num> <num> <char> <num>
#> 1: combo1 0.001000000 0.2 RV 0.957
#> 2: combo1 0.001000000 0.2 RV 0.957
#> 3: combo1 0.001000000 0.2 RV 0.957
#> 4: combo1 0.003162278 0.2 RV 0.712
#> 5: combo1 0.003162278 0.2 RV 0.712
#> ---
#> 2804: sa 1.000000000 NA GR 1.000
#> 2805: sa 1.000000000 NA GR 1.000
#> 2806: sa 1.000000000 NA GR 1.000
#> 2807: sa 1.000000000 NA GR 1.000
#> 2808: sa 1.000000000 NA GR 1.000
#> Gnumber DrugName drug_moa Gnumber_2 DrugName_2 drug_moa_2 Duration
#> <char> <char> <char> <char> <char> <char> <num>
#> 1: G00002 drug_002 moa_A G00026 drug_026 moa_E 72
#> 2: G00002 drug_002 moa_A G00026 drug_026 moa_E 72
#> 3: G00002 drug_002 moa_A G00026 drug_026 moa_E 72
#> 4: G00002 drug_002 moa_A G00026 drug_026 moa_E 72
#> 5: G00002 drug_002 moa_A G00026 drug_026 moa_E 72
#> ---
#> 2804: G00026 drug_026 moa_E <NA> <NA> <NA> 72
#> 2805: G00026 drug_026 moa_E <NA> <NA> <NA> 72
#> 2806: G00026 drug_026 moa_E <NA> <NA> <NA> 72
#> 2807: G00026 drug_026 moa_E <NA> <NA> <NA> 72
#> 2808: G00026 drug_026 moa_E <NA> <NA> <NA> 72
#> clid CellLineName Tissue ReferenceDivisionTime
#> <char> <char> <char> <num>
#> 1: CL00011 cellline_BA tissue_x 26
#> 2: CL00011 cellline_BA tissue_x 26
#> 3: CL00011 cellline_BA tissue_x 26
#> 4: CL00011 cellline_BA tissue_x 26
#> 5: CL00011 cellline_BA tissue_x 26
#> ---
#> 2804: CL00013 cellline_DA tissue_x 34
#> 2805: CL00013 cellline_DA tissue_x 34
#> 2806: CL00013 cellline_DA tissue_x 34
#> 2807: CL00013 cellline_DA tissue_x 34
#> 2808: CL00013 cellline_DA tissue_x 34
#>
#> $BM
#> 13 x 3 BumpyDataFrameMatrix
#> rownames: 1 2 ... 12 13
#> colnames: 1 2 3
#> preview [1,1]:
#> DataFrame with 90 rows and 4 columns
#> x Concentration data_source normalization_type
#> <numeric> <numeric> <character> <character>
#> 1 0.957 0.00100000 combo1 RV
#> 2 0.957 0.00100000 combo1 RV
#> 3 0.957 0.00100000 combo1 RV
#> 4 0.712 0.00316228 combo1 RV
#> 5 0.712 0.00316228 combo1 RV
#> ... ... ... ... ...
#> 86 1 0 combo1 GR
#> 87 1 0 combo1 GR
#> 88 1 0 combo1 GR
#> 89 1 0 combo1 GR
#> 90 1 0 combo1 GR
#>