Seahorse: Seahorse class constructor

In wmoldham/seahorse: Analyze Seahorse Bioenergetic Data

Seahorse class constructor

Description

Seahorse is an S4 container used to store the calibration values and raw data from a single Seahorse assay; to calculate oxygen consumption, extracellular acidification, and proton efflux rates from the raw data; and to facilitate outlier detection, data analysis, and visualization.

Usage

Seahorse(
  path,
  wells = list(),
  stages = list(),
  cells = list(),
  units = NA_character_,
  bf = NA_real_,
  cf = NA_real_
)

Arguments

path	Character vector for the Seahorse xlsx file path.
wells	An optional list or data frame containing vectors of experimental descriptors for each of the sample wells. At minimum, wells must contain character vectors named well and type. well must contain a unique entry for each well in the experimental plate. type must be sample or blank for each well. Users should consider a group column that labels unique experimental groups. It is probably worthwhile to convert this column to a factor based on the preferred ordering of experimental groups. Additional descriptors may be included (e.g., treatment, time, condition). If a group vector was not provided, one will be generated from type or a combination of the remaining descriptors.
stages	An optional list or data frame containing vectors of experimental descriptors for each of the measurement stages. stages must contain character vectors named measurement and stage. measurement must contain a unique entry for each measurement in the experiment. stage describes the experimental interval (e.g., for a typical mitochondrial stress assay, stage would be basal, oligo, fccp, or rot/ama). A well column may also be included if the injections differ among treatment wells.
cells	An optional list or data frame containing vectors of normalization data for an experiment. If provided, cells must contain a character vector named well and a numeric vector named value. well must contain a unique entry for each well in the experimental plate. value contains the normalization factor (e.g., cell number or protein content).
units	An optional character vector describing the units of the normalization factor provided in the valuecolumn of cells. This will be used to annotate graphs.
bf	An optional length-one numeric vector containing the buffer factor of the medium. This value is used to calculate the proton efflux rate (PER) from the extracellular acidification rate (ECAR).
cf	An optional length-one numeric vector describing the carbon dioxide correction factor for the cells in the assay. This parameter is used to separate the mitochondrial and glycolytic contributions to the proton efflux rate.

Details

During creation of the Seahore object, raw fluorescence readings are converted to O2 and pH measurements from which oxygen consumptions and extracellular acidification rates are calculated. Outlying wells are identified and removed.

See Also

helpers, format_cells, accessors, blanks, outliers, plot

Examples

path <- system.file("extdata/raw_1.xlsx", package = "seahorse", mustWork = TRUE)
wells <- wells_ex
stages <- stages_mst
cells <- list(well = wells_24, value = 20000)
Seahorse(path, wells, stages, cells, units = "cell", bf = 2.4, cf = 0.41)

wmoldham/seahorse documentation built on June 9, 2025, 11:36 a.m.