Package index • toxEval

Import Data

create_toxEval(): Load and check toxEval data

ToxCast Data

Data provided in the package from ToxCast database.

end_point_info: Endpoint information from ToxCast

ToxCast_ACC: ACC values included with toxEval. See vignette("Setting up toxEval package data", package = "toxEval") for more information on how the data was aggregated.

tox_chemicals: ToxCast Chemical Information

flags: ToxCast Chemical Information

Clean Data

Functions to prepare data for analysis

clean_endPoint_info(): clean_endPoint_info

get_ACC(): Get the ACC values for a selection of chemicals

get_chemical_summary(): Compute EAR values

get_concentration_summary(): Create concentration summary

remove_flags(): Remove endpoints with specific data quality flags from data

filter_groups(): Filter endPoints based on groups and assays.

graph_chem_data() tox_boxplot_data() side_by_side_data(): Prepare boxplot data

Visualize Data

Functions to create graphs and tables of output.

plot_chemical_boxplots() plot_tox_boxplots(): Grouped Boxplots

plot_tox_endpoints(): EndPoint boxplots

plot_tox_stacks(): Plot stacked bar charts

plot_tox_heatmap(): Plot EAR heat maps

hits_summary_DT() hits_summary(): Summary of hits per site/category

hits_by_groupings_DT() hits_by_groupings(): Biological hits per category

rank_sites_DT() rank_sites(): Rank sites by EAR

endpoint_hits_DT() endpoint_hits(): Rank endpoints by category

make_tox_map() map_tox_data(): Create an interactive map of the data

explore_endpoints(): Explore data in the Shiny Application

plot_tox_endpoints2(): EndPoint boxplots with faceting option

Utility Functions

Functions to help

toxEval toxEval-package: Analyze ToxCast data in relation to measured concentrations.

summary(<toxEval>): Summary of tox_list

as.toxEval(): toxEval helper functions