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Rates summary

Source: R/rate_plot.R
get_rate_summary.Rd

Summarize OCR and ECAR as mean and bounded standard deviations or standard error with confidence intervals

Usage

get_rate_summary(
  seahorse_rates,
  measure = "OCR",
  assay,
  error_metric = "ci",
  conf_int = 0.95
)

Arguments

seahorse_rates

data.table Seahorse OCR and ECAR rates (imported using read_data function)

measure

Whether to calculate summary for "OCR" or "ECAR"

assay

What assay to calculate summary for (e.g. "MITO" or "GLYCO")

error_metric

Whether to calculate error as standard deviations ("sd") or confidence intervals ("ci")

conf_int

The confidence interval percentage. Should be between 0 and 1

Value

a data.table with means, standard deviations/standard error with bounds around the mean(sd or confidence intervals)

Examples

rep_list <- system.file("extdata", package = "ceas") |>
  list.files(pattern = "*.xlsx", full.names = TRUE)
seahorse_rates <- read_data(rep_list, sheet = 2)
rates <- get_rate_summary(
  seahorse_rates,
  measure = "OCR",
  assay = "MCIO",
  error_metric = "ci",
  conf_int = 0.95
)
head(rates, n = 10)
#> Empty data.table (0 rows and 7 cols): exp_group,Measurement,mean,sd,se,lower_bound...