Load long table — load_long_table • gDRimport

Loads a long/tidy data.table from a delimited text file (CSV/TSV) and checks that it contains the columns required by the gDR pipeline. This offers an input path that does not rely on GeneDataScreeneR: the data can come from a custom export or be provided directly by the user in tabular form, matching the shape of the data_imported object used downstream.

Usage

load_long_table(long_table_file)

Arguments

long_table_file: character, path to a single CSV/TSV file with the long table. The field separator is detected automatically.

Value

a data.table with the validated long table

Details

Required columns follow the current gDR identifiers: Gnumber, clid, Duration and Concentration. The readout column is the fixed header ReadoutValue: there is no "readout" identifier in gDRutils, so this name is not customisable via get_env_identifiers(), matching how ReadoutValue is used across the rest of gDRimport. Combination data may add Gnumber_2 and Concentration_2. Duration, Concentration and ReadoutValue must be numeric.

Examples

 path <- tempfile(fileext = ".csv")
 dt <- data.table::data.table(Gnumber = "G1", clid = "CL1", Duration = 72,
                              Concentration = 1, ReadoutValue = 1000)
 data.table::fwrite(dt, path)
 load_long_table(path)
#>    Gnumber   clid Duration Concentration ReadoutValue
#>     <char> <char>    <num>         <num>        <num>
#> 1:      G1    CL1       72             1         1000