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 use. 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",
assays = c("ACEA", "APR", "ATG", "NVS", "OT", "TOX21", "CEETOX", "LTEA", "CLD",
"TANGUAY", "CCTE_PADILLA", "CCTE", "STM", "ARUNA", "CCTE_SHAFER", "CPHEA_STOKER",
"CCTE_GLTED", "UPITT", "UKN", "ERF", "TAMU", "IUF", "CCTE_MUNDY", "UTOR", "VALA"),
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
- assays
Vector of assays to use in the data analysis. Possible values are "ACEA", "APR", "ATG", "NVS", "OT", "TOX21", "CEETOX", "LTEA", "CLD", "TANGUAY", "CCTE_PADILLA", "BSK" , "CCTE", "STM", "ARUNA", "CCTE_SHAFER", "CPHEA_STOKER", "CCTE_GLTED", "UPITT", "UKN", "ERF", "TAMU", "IUF", "CCTE_MUNDY", "UTOR", "VALA". 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" directly from EPA https://www.epa.gov/chemical-research/toxcast-assay-annotation-data-user-guide. Following that link, 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)
#> endPoint groupCol assaysFull
#> 1 ACEA_ER_80hr Nuclear Receptor ACEA
#> 2 ACEA_ER_AUC_viability Cell Cycle ACEA
#> 3 APR_HepG2_CellCycleArrest_1h_dn Cell Cycle APR
#> 4 APR_HepG2_CellCycleArrest_1h_up Cell Cycle APR
#> 5 APR_HepG2_CellLoss_1h_dn Cell Cycle APR
#> 6 APR_HepG2_CellLoss_1h_up Cell Cycle APR