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.
Arguments
- ct_values
A numeric vector giving the Ct value for each observation.
- target_names
A character vector giving the target names for each element in 'ct_values'.
- standard_curves
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
template_WES_standard_curvesfor template.
Examples
df <- template_WES_data[template_WES_data$target_name == 'target_1',]
sc <- template_WES_standard_curve[template_WES_standard_curve$target_name == 'target_1',]
tmp <- calc_n_copies(ct_values = df$ct_value,
target_names = df$target_name,
standard_curves = sc)
df$n_copies <- tmp
head(df)
#> sample_date location_id lat lon target_name ct_value n_copies
#> 5 2017-06-11 1 23.80 90.37 target_1 31.60111 62.85220
#> 6 2017-06-11 1 23.80 90.37 target_1 32.20208 43.24349
#> 15 2017-06-11 2 23.80 90.38 target_1 28.91009 335.36183
#> 16 2017-06-11 2 23.80 90.38 target_1 NA NA
#> 25 2017-06-11 3 23.81 90.37 target_1 28.05273 571.73967
#> 26 2017-06-11 3 23.81 90.37 target_1 NA NA