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")
listSE <- list(
combo1 = mae[[1]],
sa = mae[[2]]
)
merge_assay(listSE, "Normalized")
#> $DT
#> data_source Concentration Concentration_2 masked normalization_type x
#> <char> <num> <num> <lgcl> <fctr> <num>
#> 1: combo1 0.001000000 0.0 FALSE RV 0.957
#> 2: combo1 0.001000000 0.2 FALSE RV 0.957
#> 3: combo1 0.001000000 1.0 FALSE RV 0.957
#> 4: combo1 0.003162278 0.0 FALSE RV 0.712
#> 5: combo1 0.003162278 0.2 FALSE RV 0.712
#> ---
#> 2804: sa 1.000000000 NA FALSE GR 1.000
#> 2805: sa 1.000000000 NA FALSE GR 1.000
#> 2806: sa 1.000000000 NA FALSE GR 1.000
#> 2807: sa 1.000000000 NA FALSE GR 1.000
#> 2808: sa 1.000000000 NA FALSE 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 54 rows and 5 columns
#> masked x Concentration data_source normalization_type
#> <logical> <numeric> <numeric> <character> <factor>
#> 1 FALSE 0.9570 0.00100000 combo1 RV
#> 2 FALSE 0.4519 0.01000000 combo1 GR
#> 3 FALSE 0.4519 0.01000000 combo1 GR
#> 4 FALSE 0.7120 0.00316228 combo1 RV
#> 5 FALSE 0.3691 0.03162278 combo1 GR
#> ... ... ... ... ... ...
#> 50 FALSE 0.1863 10.00000000 combo1 RV
#> 51 FALSE 0.7691 0.00316228 combo1 GR
#> 52 FALSE 0.1866 3.16227766 combo1 RV
#> 53 FALSE 0.1863 10.00000000 combo1 RV
#> 54 FALSE 0.1866 3.16227766 combo1 RV
#>