calc_n_copies

This function calculates the quantitative value of the qPCR Ct value. Cycle threshold here is converted into
the estimated number of gene target copies (e.g. viral load for a viral pathogen) by fitting a log linear model
to the standard curve data and then using that model to find a point estimate for the provided Ct values.

Provides reproducible functions for collating and analyzing
data from environmental sampling studies. Environmental Sampling (ES)
of infectious diseases involves collecting samples from various sources
(such as sewage, water, air, soil, or surfaces) to monitor the presence
of pathogens in the environment. Analysis of ES data often requires the
calculation of Real-Time Quantitative PCR (qPCR) variables, normalizing
ES observations, and analyzing sampling site characteristics. To help
reduce the complexity of these analyses we have implemented tools that
assist with establishing standardized ES data formats, absolute and
relative quantification of qPCR data, estimation of qPCR amplification
efficiency, and collating open-source spatial data for sampling sites.

John R Giles

Tools for Analyzing Wastewater and Environmental Sampling Data

calc_n_copies function

<dl><dt>ct_values</dt>
<dd>A numeric vector giving the Ct value for each observation.</dd>
<dt>target_names</dt>
<dd>A character vector giving the target names for each element in 'ct_values'.</dd>
<dt>standard_curves</dt>
<dd>A data.frame containing results from standard curve dilution experiment.
Elements in 'target_names' must map to either 'target_name_unique' or 'target_name_concise'. See package
data object <code>template_WES_standard_curves</code> for template.</dd></dl>

Arguments

Calculate number of target copies — calc_n_copies

<dl>

<dt>ct_values</dt>
<dd>A numeric vector giving the Ct value for each observation.</dd>


<dt>target_names</dt>
<dd>A character vector giving the target names for each element in 'ct_values'.</dd>


<dt>standard_curves</dt>
<dd>A data.frame containing results from standard curve dilution experiment.
Elements in 'target_names' must map to either 'target_name_unique' or 'target_name_concise'. See package
data object <code>template_WES_standard_curves</code> for template.</dd>

</dl>

calc_n_copies: Calculate number of target copies

Description

Usage

Value

Arguments

Examples