Skip to contents

Convert assay readings to titers

Source: R/to_titer.R
to_titer.Rd

to_titer() converts raw assay readings (e.g., OD, fluorescence intensity) to titer by fitting a calibrating model

Usage

to_titer(
  df,
  model = "4PL",
  positive_threshold = NULL,
  ci = 0.95,
  negative_control = TRUE
)

Arguments

df

a standardized data.frame returned by`standardize_data()`

model

either:

  1. A string naming a built-in model (currently supported: "4PL"), or

  2. A named list with two functions: $mod for curve fitting and $quantify_ci for titer estimation with confidence intervals.

positive_threshold

if not NULL, processed_data will have the serostatus labeled

ci

confidence interval for the titer estimates (default is .95 i.e., 95% CI)

negative_control

if TRUE, output tibble will include the result for negative controls

Value

a data.frame with 8 columns

plate_id

id of the plate

data

list of `data.frame`s containing the raw sample results from each plate

antitoxin_df

list of `data.frame`s containing the raw results for antitoxins from each plate

standard_curve_func

list of functions mapping from assay reading to titer for each plate

std_crv_midpoint

midpoint of the standard curve, for qualitative analysis

processed_data

list of `tibble`s containing samples with titer estimates (lower, median, upper)

negative_control

list of `tibble`s containing negative control check results (if `negative_control=TRUE`)