clean_endPoint_info: clean_endPoint_info

In USGS-R/toxEval: Exploring Biological Relevance of Environmental Chemistry Observations

clean_endPoint_info

Description

Define a subset of the ToxCast database for relevance to toxEval analyses. Subsetting is done based upon methods defined by Blackwell et al., 2017 ( \Sexpr[results=rd]{tools:::Rd_expr_doi("10.1021/acs.est.7b01613")}). Specifically, this function removes endPoints that are ATG sources with signal loss, and NVS with signal gain (basically: some assay/signal combinations are removed because they target non-specific endpoints). Also, this function adds additional categories to intended_target_family and intended_target_family_sub as described in the paper linked above.

Usage

clean_endPoint_info(end_point_info)

Arguments

end_point_info

Data frame Endpoint information from ToxCast.

Value

The returned data frame is based on end_point_info, but with some endPoints filtered out and some additional categories in intended_target_family and intended_target_family_sub. The names in intended_target_family are revised to look more appealing in graphs and tables.

Examples

end_point_info <- end_point_info
nrow(end_point_info)
cleaned_ep <- clean_endPoint_info(end_point_info)
nrow(cleaned_ep)

USGS-R/toxEval documentation built on Feb. 9, 2024, 6:24 p.m.