calc_analyte_mfi: Calculate the analyte intensity

In beadplexr: Analysis of Multiplex Cytometric Bead Assays

Calculate the analyte intensity

Description

The mean fluorescence intensity (MFI) of the analyte

Usage

calc_analyte_mfi(
  df,
  .parameter,
  .column_name = "analyte",
  .mean_fun = c("geometric", "harmonic", "arithmetic"),
  .data = NULL
)

Arguments

df	A tidy data.frame.
.parameter	A character giving the name of column(s) where populations are identified.
.column_name	A character giving the name of the column to store the population information.
.mean_fun	A character giving the mean function to use.
.data	Deprecated. Use df.

Value

A summarized data.frame

Mean calculation

The calculation of the harmonic mean is as follows:

n\frac{1}{\sum_{i=1}^n \frac{1}{x_i}}

NAs are removed before calculation

The geometric mean is given by:

\left(\prod_{i=1}^n x_i \right)^\frac{1}{n}

but implemented as:

\frac{1}{n}\exp{\sum_{i=1}^n\log(x_i)}

NAs are removed before calculation

Examples

library(beadplexr)
library(dplyr)

data("lplex")

df <- lplex[[1]] |>
  filter(`FSC-A` > 4e5L, `FSC-A` < 6.3e5L) |>
  identify_analyte(.parameter = "FL6-H",
                   .analyte_id = as.character(c(1:7)))

df |>
  calc_analyte_mfi(.parameter = "FL2-H")

df |>
  calc_analyte_mfi(.parameter = "FL2-H",
              .mean_fun = "harmonic")

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