View source: R/get_chemical_summary.R
get_chemical_summary | R Documentation |
This function computes Exposure:Activity ratios using user-provided measured
concentration data from the output of create_toxEval
,
and joins the data with the activity concentration at cutoff data provided by
ToxCast.Data from ToxCast is included with this package, but alternative
benchmark data can be provided to perform the same "toxEval" analysis.
get_chemical_summary(
tox_list,
ACC = NULL,
filtered_ep = "All",
chem_data = NULL,
chem_site = NULL,
chem_info = NULL,
exclusion = NULL
)
tox_list |
List with data frames for chem_data, chem_info, chem_site,
and optionally exclusions and benchmarks. Created with |
ACC |
Data frame with columns: CAS, chnm, endPoint, and ACC_value
for specific chemical/endpoint combinations generated using the
|
filtered_ep |
Data frame with columns: endPoints, groupCol. Default is |
chem_data |
Optional data frame with (at least) columns: CAS, SiteID, and Value. Default is |
chem_site |
Optional data frame with (at least) columns: SiteID, and Short Name. Default is |
chem_info |
Optional data frame with (at least) columns: CAS, and class. Default is |
exclusion |
Optional data frame with (at least) columns: CAS and endPoint. Default is |
To use the data provided by the package, a sample workflow is shown below in the examples. The examples include retrieving the ToxCast (ACC) values that are used to calculate EARs, choosing endPoints that should be ignored based on data quality "flags" in the ToxCast database, and removing groups of endPoints that may not be important to the analysis at hand.
a data frame with the columns: CAS, chnm (chemical name as a factor), site, date, EAR, Bio_category, shortName (of site), Class. The output of this function is where you find EAR values for every chemical/endpoint combination.
path_to_tox <- system.file("extdata", package = "toxEval")
file_name <- "OWC_data_fromSup.xlsx"
full_path <- file.path(path_to_tox, file_name)
tox_list <- create_toxEval(full_path)
ACC <- get_ACC(tox_list$chem_info$CAS)
ACC <- remove_flags(ACC)
cleaned_ep <- clean_endPoint_info(end_point_info)
filtered_ep <- filter_groups(cleaned_ep)
chemical_summary <- get_chemical_summary(tox_list, ACC, filtered_ep)
head(chemical_summary)
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