Convert a MultiAssayExperiment assay to a long data.table
Source:R/convert_mae_se_assay_to_dt.R
convert_mae_assay_to_dt.RdConvert an assay within a SummarizedExperiment object in a MultiAssayExperiment to a long data.table.
Usage
convert_mae_assay_to_dt(
mae,
assay_name,
experiment_name = NULL,
include_metadata = TRUE,
retain_nested_rownames = FALSE,
wide_structure = FALSE,
drop_masked = TRUE
)Arguments
- mae
A MultiAssayExperiment object holding experiments with raw and/or processed dose-response data in its assays.
- assay_name
String of name of the assay to transform within an experiment of the
mae.- experiment_name
String of name of the experiment in
maewhoseassay_nameshould be converted. Defaults toNULLto indicate to convert assay in all experiments into one data.table object.- include_metadata
Boolean indicating whether or not to include
rowData()andcolData()in the returned data.table. Defaults toTRUE.- retain_nested_rownames
Boolean indicating whether or not to retain the rownames nested within a
BumpyMatrixassay. Defaults toFALSE. If theassay_nameis not of theBumpyMatrixclass, this argument's value is ignored. IfTRUE, the resulting column in the data.table will be named as"<assay_name>_rownames".- wide_structure
Boolean indicating whether or not to transform data.table into wide format.
wide_structure = TRUErequiresretain_nested_rownames = TRUEhowever that will be validated inconvert_se_assay_to_dtfunction- drop_masked
Boolean indicating whether to drop masked values; TRUE by default.
Details
NOTE: to extract information about 'Control' data, simply call the function with the name of the assay holding data on controls.
Author
Bartosz Czech bartosz.czech@contractors.roche.com
Examples
mae <- get_synthetic_data("finalMAE_small")
convert_mae_assay_to_dt(mae, "Metrics")
#> rId cId x_mean
#> <char> <char> <num>
#> 1: G00002_drug_002_moa_A_72 CL00011_cellline_BA_tissue_x_26 0.4466890
#> 2: G00002_drug_002_moa_A_72 CL00011_cellline_BA_tissue_x_26 0.4729298
#> 3: G00003_drug_003_moa_A_72 CL00011_cellline_BA_tissue_x_26 0.3939872
#> 4: G00003_drug_003_moa_A_72 CL00011_cellline_BA_tissue_x_26 0.3932199
#> 5: G00004_drug_004_moa_A_72 CL00011_cellline_BA_tissue_x_26 0.7989283
#> ---
#> 196: G00009_drug_009_moa_A_72 CL00020_cellline_KB_tissue_z_62 0.0774842
#> 197: G00010_drug_010_moa_A_72 CL00020_cellline_KB_tissue_z_62 0.5769999
#> 198: G00010_drug_010_moa_A_72 CL00020_cellline_KB_tissue_z_62 0.1991504
#> 199: G00011_drug_011_moa_B_72 CL00020_cellline_KB_tissue_z_62 0.4117805
#> 200: G00011_drug_011_moa_B_72 CL00020_cellline_KB_tissue_z_62 -0.1148134
#> x_AOC x_AOC_range xc50 x_max ec50 x_inf
#> <num> <num> <num> <num> <num> <num>
#> 1: 0.5533110 0.6277120 0.007253171 0.32793333 0.003795893 0.34682665
#> 2: 0.5270702 0.6048472 0.008956223 0.33660000 0.004512560 0.36516781
#> 3: 0.6060128 0.6954994 0.005655581 0.27413333 0.003962986 0.28319787
#> 4: 0.6067801 0.7027714 0.006591468 0.25136667 0.004714084 0.26639679
#> 5: 0.2010717 0.2385432 Inf 0.70636667 0.016546380 0.71001484
#> ---
#> 196: 0.9225158 1.0742560 0.026077313 -0.49686667 0.037516853 -0.52393526
#> 197: 0.4230001 0.4723104 0.150209032 0.07513333 0.137152296 0.09235428
#> 198: 0.8008496 0.8915995 0.096729600 -0.78626667 0.146270629 -0.74430401
#> 199: 0.5882195 0.6900581 0.027440547 0.08603333 0.024485958 0.09662172
#> 200: 1.1148134 1.3059605 0.016239553 -0.76026667 0.026434030 -0.73401896
#> x_0 h r2 p_value rss maxlog10Concentration
#> <num> <num> <num> <num> <num> <num>
#> 1: 1 1.827031 0.9924695 3.705769e-08 0.002778822 1
#> 2: 1 1.911901 0.9884406 1.660656e-07 0.004530345 1
#> 3: 1 2.349599 0.9958511 4.600131e-09 0.002182340 1
#> 4: 1 2.270093 0.9905292 8.267143e-08 0.005670066 1
#> 5: 1 3.159939 0.9918874 4.809026e-08 0.001162341 1
#> ---
#> 196: 1 1.970723 0.9955609 5.828304e-09 0.017400921 1
#> 197: 1 2.245643 0.9988156 5.718652e-11 0.001842420 1
#> 198: 1 2.204685 0.9985705 1.104466e-10 0.008161064 1
#> 199: 1 1.884916 0.9986615 8.773134e-11 0.001844621 1
#> 200: 1 1.854308 0.9987249 7.403286e-11 0.006484241 1
#> N_conc x_sd_avg fit_type normalization_type fit_source
#> <int> <num> <char> <char> <char>
#> 1: 9 0.02424423 DRC3pHillFitModelFixS0 RV gDR
#> 2: 9 0.03203268 DRC3pHillFitModelFixS0 GR gDR
#> 3: 9 0.02195104 DRC3pHillFitModelFixS0 RV gDR
#> 4: 9 0.03075240 DRC3pHillFitModelFixS0 GR gDR
#> 5: 9 0.02315049 DRC3pHillFitModelFixS0 RV gDR
#> ---
#> 196: 9 0.04602459 DRC3pHillFitModelFixS0 GR gDR
#> 197: 9 0.03151223 DRC3pHillFitModelFixS0 RV gDR
#> 198: 9 0.06333498 DRC3pHillFitModelFixS0 GR gDR
#> 199: 9 0.03335063 DRC3pHillFitModelFixS0 RV gDR
#> 200: 9 0.07007818 DRC3pHillFitModelFixS0 GR gDR
#> Gnumber DrugName drug_moa Duration clid CellLineName Tissue
#> <char> <char> <char> <num> <char> <char> <char>
#> 1: G00002 drug_002 moa_A 72 CL00011 cellline_BA tissue_x
#> 2: G00002 drug_002 moa_A 72 CL00011 cellline_BA tissue_x
#> 3: G00003 drug_003 moa_A 72 CL00011 cellline_BA tissue_x
#> 4: G00003 drug_003 moa_A 72 CL00011 cellline_BA tissue_x
#> 5: G00004 drug_004 moa_A 72 CL00011 cellline_BA tissue_x
#> ---
#> 196: G00009 drug_009 moa_A 72 CL00020 cellline_KB tissue_z
#> 197: G00010 drug_010 moa_A 72 CL00020 cellline_KB tissue_z
#> 198: G00010 drug_010 moa_A 72 CL00020 cellline_KB tissue_z
#> 199: G00011 drug_011 moa_B 72 CL00020 cellline_KB tissue_z
#> 200: G00011 drug_011 moa_B 72 CL00020 cellline_KB tissue_z
#> ReferenceDivisionTime
#> <num>
#> 1: 26
#> 2: 26
#> 3: 26
#> 4: 26
#> 5: 26
#> ---
#> 196: 62
#> 197: 62
#> 198: 62
#> 199: 62
#> 200: 62