Read perpetrator information from file or text string

The input source can either be a file name as string or a text connection. This can be used to read the compound data from a string.

Usage

read_perpetrators(source)

Arguments

source: The file name or text connection to read from.

Value

A perpetrator object if only one compound in the input source, or list of perpetrator objects.

Details

The following fields are expected in the input (in this order):

'name' The compound name as character.
'parameter' The parameter as character.
'value' The respective value as character.
'source' Optional source information as character.

The following parameters are expected:

'oral' A Boolean (i.e., TRUE or FALSE) to indicate whether the drug is subject to first-pass effects.
'mw' The molar weight in g/mol as numeric.
'dose' The clinically administered dose in mg as numeric.
'imaxss' The (total) \(C_{max}\) in ng/ml after administration of the clinical dose.
'fu' The free unbound) fraction of the drug in plasma.
'fumic' The free (unbound) fraction in microsomal preparations.
'rb' The blood-to-plasma concentration ratio.
'fa' The fraction absorbed of the drug.
'fg' The fraction of the administered dose escaping gut metabolism.
'ka' The absorption rate constant in 1/min.
'solubility' The aqueous solubility of the compound in mg/l.

Lines starting with '#' are considered comments and are not evaluated.

Note that multiple compounds, e.g., the parent and metabolites may be included in the perpetrator file. The below is an example of a valid compound file:

    # PARENT
    # compound,  param,    value,     source
    examplinib,  oral,     TRUE,
    examplinib,  mw,       492.6,
    examplinib,  dose,     450,       clinical dose
    examplinib,  imaxss,   3530,      study 001
    examplinib,  fu,       0.023,     study 002
    examplinib,  fumic,    1,         default
    examplinib,  rb,       1,         study 003
    examplinib,  fa,       0.81,      study 003
    examplinib,  fg,       1,         default
    examplinib,  ka,       0.00267,   unknown

    # METABOLITE
    # compound,  param,    value,     source
    M1,          oral,     FALSE,
    M1,          mw,       506.56,
    M1,          dose,     NA,
    M1,          imaxss,   1038,      study 001
    M1,          fu,       0.012,     study 002
    M1,          fumic,    1,         default
    M1,          rb,       1,         study 002
    M1,          fa,       NA,
    M1,          fg,       NA,
    M1,          ka,       NA,

Examples

read_perpetrators(textConnection(examplinib_compounds_string))
#> $M1
#> ----- DDI perpetrator object -----
#> name         M1                   
#> oral         FALSE                
#> mw           506.56               
#> dose         NA                   
#> imaxss       1038     study 001   
#> fu           0.012    study 002   
#> fumic        1        default     
#> rb           1        study 002   
#> fa           NA                   
#> fg           NA                   
#> ka           NA                   
#> solubility   Inf      default
#> $examplinib
#> ----- DDI perpetrator object -----
#> name         examplinib                   
#> oral         TRUE                         
#> mw           492.6                        
#> dose         450          clinical dose   
#> imaxss       3530         study 001       
#> fu           0.023        study 002       
#> fumic        1            default         
#> rb           1            study 003       
#> fa           0.81         study 003       
#> fg           1            default         
#> ka           0.00267      unknown         
#> solubility   Inf          default