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.
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")
)Data frame containing Endpoint information from ToxCast
Character name of ToxCast annotation column to use as a group category
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.
Vector of groups within the selected 'groupCol' to remove.
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.
end_point_info <- end_point_info
cleaned_ep <- clean_endPoint_info(end_point_info)
filtered_ep <- filter_groups(cleaned_ep)
head(filtered_ep)
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