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Filter endPoints based on groups and assays.

Source: R/filter_endPoint_info.R
filter_groups.Rd

This function provides a mechanism to specify 3 levels of information in the supplied data frame end_point_info to be used in subsequent analysis steps. First, the user specifies the ToxCast assay annotation using the 'groupCol' argument, which is a column header in 'end_point_info'. Second, the user specifies the families of assays to exclude. Finally, the user can choose to remove specific group(s) from the category. The default is to remove 'Background Measurement' and 'Undefined'. Choices for this should be reconsidered based on individual study objectives.

Usage

filter_groups(
  ep,
  groupCol = "intended_target_family",
  remove_assays = c("BSK"),
  remove_groups = c("Background Measurement", "Undefined")
)

Arguments

ep

Data frame containing Endpoint information from ToxCast

groupCol

Character name of ToxCast annotation column to use as a group category

remove_assays

Vector of assays to EXCLUDE in the data analysis. By default, the "BSK" (BioSeek) assay is removed.

remove_groups

Vector of groups within the selected 'groupCol' to remove.

Details

The default category ('groupCol') is 'intended_target_family'. Depending on the study, other categories may be more relevant. The best resource on these groupings is the "ToxCast Assay Annotation Data User Guide". It defines "intended_target_family" as "the target family of the objective target for the assay". Much more detail can be discovered in that documentation.

Examples

end_point_info <- end_point_info
cleaned_ep <- clean_endPoint_info(end_point_info)
filtered_ep <- filter_groups(cleaned_ep)
head(filtered_ep)
#> # A tibble: 6 × 3
#>   endPoint                      groupCol         assaysFull
#>   <chr>                         <chr>            <chr>     
#> 1 ACEA_ER_80hr                  Nuclear Receptor ACEA      
#> 2 APR_HepG2_CellCycleArrest_1hr Cell Cycle       APR       
#> 3 APR_HepG2_CellLoss_1hr        Cell Cycle       APR       
#> 4 APR_HepG2_MicrotubuleCSK_1hr  Cell Morphology  APR       
#> 5 APR_HepG2_MitoMass_1hr        Cell Morphology  APR       
#> 6 APR_HepG2_MitoMembPot_1hr     Cell Morphology  APR