get_energetics_summary: Calculate ATP Production Mean and Standard Deviation

In ceas: Cellular Energetics Analysis Software

Calculate ATP Production Mean and Standard Deviation

Description

Calculates mean and standard deviation of ATP production from glycolysis and OXPHOS at points defined in partition_data and with values calculated using the get_energetics function via ordinary least squares or a mixed-effects model

Usage

get_energetics_summary(
  energetics,
  model = "ols",
  error_metric = "ci",
  conf_int = 0.95,
  sep_reps = FALSE,
  ci_method = "Wald"
)

Arguments

energetics	a data.table of Seahorse OCR and ECAR rates (from get_energetics)
model	The model used to estimate mean and confidence intervals: ordinary least squares ("ols") or mixed-effects ("mixed")
error_metric	Whether to calculate error as standard deviation ("sd") or confidence intervals ("ci")
conf_int	The confidence interval percentage. Should be between 0 and 1
sep_reps	Whether to calculate summary statistics on the groups with replicates combined. The current default FALSE combines replicates, but future releases will default to TRUE providing replicate-specific summaries.
ci_method	The method used to compute confidence intervals for the mixed-effects model: "Wald", "profile", or "boot" passed to lme4::confint.merMod().

Details

To get the means and confidence intervals for experiments with replicates, users can either use sep_reps = TRUE to get replicate-level summary statistics or set model = "mixed" to use a linear mixed-effects model on with replicate as the random-effect. The confidence intervals are generated using confint(method = "Wald").

Value

a list of groups from the data

Examples

rep_list <- system.file("extdata", package = "ceas") |>
  list.files(pattern = "*.xlsx", full.names = TRUE)
seahorse_rates <- read_data(rep_list, sheet = 2)
partitioned_data <- partition_data(seahorse_rates)
energetics_list <- get_energetics(
  partitioned_data,
  ph = 7.4,
  pka = 6.093,
  buffer = 0.1
)
energetics_summary <- get_energetics_summary(energetics_list, sep_reps = FALSE)
head(energetics_summary[, c(1:5)], n = 10)
head(energetics_summary[, c(1, 2, 6, 7)], n = 10)

ceas documentation built on April 3, 2025, 8:34 p.m.