gtoxSubsetChid {GladiaTOX} | R Documentation

## Subset level 5 data to a single sample per chemical

### Description

`gtoxSubsetChid` subsets level 5 data to a single tested sample per chemical. In other words, if a chemical is tested more than once (a chid has more than one spid) for a given assay endpoint, the function uses a series of logic to select a single "representative" sample.

### Usage

    gtoxSubsetChid(dat, flag = TRUE)

### Arguments

`dat` | data.table, a data.table with level 5 data
`flag` | Integer, the mc6_mthd_id values to go into the flag count, see details for more information

### Details

`gtoxSubsetChid` is intended to work with level 5 data that has chemical and assay information mapped with `gtoxPrepOtpt`.

To select a single sample, first a "consensus hit-call" is made by majority rule, with ties defaulting to active. After the chemical-wise hit call is made, the samples corresponding to to chemical-wise hit call are logically ordered using the fit category, the number of the flags, and the modl_ga, then the first sample for every chemical is selected.

The `flag` param can be used to specify a subset of flags to be used in the flag count. Leaving `flag` TRUE utilize all the available flags. Setting `flag` to `FALSE` will do the subsetting without considering any flags.

### Value

A data.table with a single sample for every given chemical-assay pair.

### See Also

`gtoxPrepOtpt`

### Examples

    ## Store the current config settings, so they can be reloaded at the end
    ## of the examples
    conf_store <- gtoxConfList()
    gtoxConfDefault()

    ## Load the example level 5 data
    d1 <- gtoxLoadData(lvl = 5, fld = "aeid", val = 2)
    d1 <- gtoxPrepOtpt(d1)

    ## Subset to an example of a duplicated chid
    d2 <- d1[chid == 10]
    d2[ , list(m4id, hitc, fitc, modl_ga)]

    ## Here the consensus hit-call is 1 (active), and the fit categories are
    ## all equal. Therefore, if the flags are ignored, the selected sample will
    ## be the sample with the lowest modl_ga.
    gtoxSubsetChid(dat = d2, flag = FALSE)[ , list(m4id, modl_ga)]

    ## Reset configuration
    options(conf_store)

[Package GladiaTOX version 1.4.0 Index]