calc_std_conc: Calculate standard concentration

In beadplexr: Analysis of Multiplex Cytometric Bead Assays

Calculate standard concentration

Description

Given a start concentration and dilution factor, the concentration of the given standard samples is calculated

Usage

calc_std_conc(.standard_sample, .start_concentration, .dilution_factor = 4L)

Arguments

.standard_sample	a vector giving the standard samples. The sample with the highest value is given the start concentration, and a .standard_sample with the value of 0, is set to 0 if it exists. See Details for details on how order is assessed.
.start_concentration	a numeric vector giving the initial standard concentration. If longer than one the maximum value is taken as start concentration.
.dilution_factor	a numeric vector giving the dilution factor. If a single element is passed, this is applied to all standard samples as a dilution series. If more then one value is given, it must be of equal length as the .standard_sample, and each element is taken as the dilution factor to the previous element, using 1 for the first element. The order of dilution factors must match that of the ordered .standard_sample.

Details

In the manuals to the LEGENDplex system, standard are labeled 0 to 8, where 8 indicate the highest concentration and 0 the background (no analyte). The standard is diluted at 1:4 so that

[s7] = [start]
[s6] = [s7]/4
[s5] = [s6]/4
[s4] = [s5]/4
[s3] = [s4]/4
[s2] = [s3]/4
[s1] = [s2]/4
[s0] = 0

It might happen, that a dilution step is missing in which case the dilution is corrected to accommodate the missing step. However, since it is inspired guess work and out of the ordinary, a warning is thrown, see Examples.

Value

A numeric vector

Standard sample order

If the vector is numeric, the values are ordered numerically from high to low.

If the vector is not numeric, things become a little more difficult, because sorting a vector like c("a", "c", "0", "b") by default results in c("0", "a", "b", "c"), which means that '0' is the highest value and will be assigned the start concentration and the sample 'a' is then the first dilution.

To avoid this problem, the vector is split into two: one containing numerical values and one containing alphabetical. Each vector is then sorted appropriately and combined, see Examples.

Examples

calc_std_conc(.standard_sample = c(7:0),
                                 .start_concentration = 5000)

suppressWarnings(
# Sample 5 is missing - raises a warning
calc_std_conc(.standard_sample = c(7, 6, 4, 3, 2, 1, 0),
                                 .start_concentration = 5000)
)

calc_std_conc(.standard_sample = rep(c(7:0), 2),
                                 .start_concentration = 5000)
calc_std_conc(.standard_sample = c(9:0),
                                .start_concentration = 5000)

calc_std_conc(.standard_sample = c(letters[1:7], 0),
                                 .start_concentration = 5000)
calc_std_conc(.standard_sample = c(letters[1:7], 0, 1),
                                 .start_concentration = 5000)

calc_std_conc(.standard_sample = c(7:1, 0),
                                 .start_concentration = 5000,
                                 .dilution_factor = c(1, 2, 2, 2, 4, 6, 6, 0))

# If 0 exists it is always set to 0
calc_std_conc(.standard_sample = c(7:1, 0),
                                 .start_concentration = 5000,
                                 .dilution_factor = c(1, 2, 2, 2, 4, 6, 6, 100000))
calc_std_conc(.standard_sample = c(8:1),
                                 .start_concentration = 5000,
                                 .dilution_factor = c(1, 2, 2, 2, 4, 6, 6, 100000))

beadplexr documentation built on July 9, 2023, 5:59 p.m.