rates_lme_summary: Estimate mean and confidence intervals for ATP measures using...

In ceas: Cellular Energetics Analysis Software

Estimate mean and confidence intervals for ATP measures using a mixed-effects model

Description

Estimates 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

Usage

rates_lme_summary(measure, assay, rates, conf_int, ci_method)

Arguments

measure	Whether to plot "OCR" or "ECAR"
assay	What assay to plot (e.g. "MITO" or "GLYCO")
rates	a data.table of Seahorse OCR and ECAR rates (from get_energetics)
conf_int	The confidence interval percentage. Should be between 0 and 1
ci_method	The method used to compute confidence intervals for the mixed-effects model: "Wald", "profile", or "boot" passed to lme4::confint.merMod().

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)
rates_lme_summary(
  measure = "OCR",
  assay = "MITO",
  rates = seahorse_rates,
  conf_int = 0.95,
  ci_method = "Wald"
)

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