zfishdev

The datasets contain 4 toxicity endpoints and 3 chemicals.

datasets

An R interface for processing concentration-response datasets using Curvep, a response noise filtering algorithm. The algorithm was described in the publications (Sedykh A et al. (2011) <doi:10.1289/ehp.1002476> and Sedykh A (2016) <doi:10.1007/978-1-4939-6346-1_14>). Other parametric fitting approaches (e.g., Hill equation) are also adopted for ease of comparison. 3-parameter Hill equation from 'tcpl' package (Filer D et al., <doi:10.1093/bioinformatics/btw680>) and 4-parameter Hill equation from Curve Class2 approach (Wang Y et al., <doi:10.2174/1875397301004010057>) are available. Also, methods for calculating the confidence interval around the activity metrics are also provided. The methods are based on the bootstrap approach to simulate the datasets (Hsieh J-H et al. <doi:10.1093/toxsci/kfy258>). The simulated datasets can be used to derive the baseline noise threshold in an assay endpoint. This threshold is critical in the toxicological studies to derive the point-of-departure (POD).

Jui-Hua Hsieh

Rcurvep

Concentration-Response Data Analysis using Curvep

Alexander Sedykh

Fred Parham

Yuhong Wang

Tongan Zhao

Ruili Huang

zfishdev function

A tibble with 96 rows and 5 columns:
<dl>
<dt>endpoint</dt>
<dd>endpoint name + at time point measured</dd><dt>chemical</dt>
<dd>chemical name + CASRN</dd><dt>conc</dt>
<dd>concentrations in log10(M) format</dd><dt>n_in</dt>
<dd>number of incidence</dd><dt>N</dt>
<dd>number of embryos</dd>
</dl>

Format

Subsets of concentration response datasets from zebrafish developmental toxicity assays — zfishdev

A tibble with 96 rows and 5 columns:
<dl>
<dt>endpoint</dt>
<dd>endpoint name + at time point measured</dd>

<dt>chemical</dt>
<dd>chemical name + CASRN</dd>

<dt>conc</dt>
<dd>concentrations in log10(M) format</dd>

<dt>n_in</dt>
<dd>number of incidence</dd>

<dt>N</dt>
<dd>number of embryos</dd>


</dl>

zfishdev: Subsets of concentration response datasets from zebrafish developmental toxicity assays

Description

Usage

Arguments

Format