Load, convert and process the level 6 PRISM data into a gDR input

Load, convert and process the level 6 PRISM data into a gDR input

Usage

convert_LEVEL6_prism_to_gDR_input(
  prism_data_path,
  cell_line_data_path,
  treatment_data_path,
  readout_min = 1.03
)

Arguments

prism_data_path

path to PRISM LEVEL6 csv file with collapsed log fold change data

cell_line_data_path

path to cell line info data

treatment_data_path

path to collapsed treatment info data

readout_min

minimum ReadoutValue

Value

data.table object with input data for gDR pipeline

Examples

 prism_data_path <- system.file("testdata/prism_collapsed_LOGFC.csv", package = "gDRimport")
 cell_line_data_path <- system.file("testdata/prism_cell_lines.csv", package = "gDRimport")
 treatment_data_path <- system.file("testdata/prism_treatment.csv", package = "gDRimport")
 convert_LEVEL6_prism_to_gDR_input(prism_data_path, cell_line_data_path, treatment_data_path)
#>         clid             Gnumber            DrugName      drug_moa Duration
#>       <char>              <char>              <char>        <char>    <num>
#> 1: some_clid some_drug_name_run1 some_drug_name_run1 some_drug_moa      120
#> 2: some_clid some_drug_name_run2 some_drug_name_run2 some_drug_moa      120
#> 3: some_clid             vehicle             vehicle       vehicle      120
#>    Concentration ReadoutValue masked CellLineName Tissue parental_identifier
#>            <num>        <num> <lgcl>       <char> <char>              <char>
#> 1:      2.325889    0.9892612  FALSE    some_clid   clid             unknown
#> 2:      2.325889    0.9330330  FALSE    some_clid   clid             unknown
#> 3:      0.000000    1.0000000  FALSE    some_clid   clid             unknown
#>    subtype ReferenceDivisionTime
#>     <char>                 <num>
#> 1: unknown                    NA
#> 2: unknown                    NA
#> 3: unknown                    NA