accessors: Accessors for 'seahorse' S4 objects

In wmoldham/seahorse: Analyze Seahorse Bioenergetic Data

Accessors for seahorse S4 objects

Description

These functions describe how to access and replace values in Seahorse and Herd objects.

Usage

## S4 method for signature 'Seahorse'
bf(x)

## S4 replacement method for signature 'Seahorse'
bf(x) <- value

## S4 method for signature 'Seahorse'
cells(x)

## S4 replacement method for signature 'Seahorse'
cells(x) <- value

## S4 method for signature 'Seahorse'
cf(x)

## S4 replacement method for signature 'Seahorse'
cf(x) <- value

## S4 method for signature 'Seahorse'
filename(x)

## S4 method for signature 'Seahorse'
stages(x)

## S4 replacement method for signature 'Seahorse'
stages(x) <- value

## S4 method for signature 'Seahorse'
units(x)

## S4 replacement method for signature 'Seahorse'
units(x) <- value

## S4 method for signature 'Herd'
units(x)

## S4 replacement method for signature 'Herd'
units(x) <- value

## S4 method for signature 'Seahorse'
wells(x)

## S4 replacement method for signature 'Seahorse'
wells(x) <- value

Arguments

x	A Seahorse or Herd object.
value	A replacement value.

Details

Format of value for the class replacement methods:

⁠bf:⁠

A 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).

⁠cells:⁠

A list or data frame containing normalization data for an experiment. 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).

⁠cf:⁠

A length-one numeric vector describing the CO2 correction factor for the cells in the assay. This parameter is used to separate the mitochondrial and glycolytic contributions to the proton efflux rate.

⁠stages:⁠

A list or data frame containing vectors of experimental descriptors for each of the measurement stages. At minimum, 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, rot/ama). A well column may also be included if the injections differ across the plate.

⁠units:⁠

A character vector describing the units of the normalization factor provided in the value column of cells. This will be used to annotate graphs.

⁠units:⁠

A character vector describing the units of the normalization factor. This will be used to annotate graphs.

⁠wells:⁠

A list or data frame containing vectors of experimental descriptors for each of the sample wells. 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. Additional descriptors may be included (e.g., treatment, time, condition, etc.). The experimental data provided will be converted to a data frame. If a group vector was not provided, one will be generated from type or a combination of the remaining descriptors. Assigning an empty list with ⁠wells<-⁠ will restore the assignment based on the raw data file.

Value

bf(x) returns the medium buffer factor.

cells(x) returns the normalization values used to adjust the rate measurements.

cf(x) returns the carbon dioxide correction factor.

filename(x) returns the base filename for the Seahorse experiment.

stages(x) returns the experimental design details associated with each stage.

units(x) returns the character vector describing the normalization units.

units(x) returns the character vector describing the normalization units.

wells(x) returns the experimental design details associated with each well.

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