analysis: Accessors for analysis output

In wmoldham/seahorse: Analyze Seahorse Bioenergetic Data

Accessors for analysis output

Description

These functions access calculated values from Seahorse or Herd objects. Collecting Seahorse objects into a Herd returns one average value for each group from each Seahorse experiment. For example, summary(Seahorse) returns summarized values for each stage from each well, while summary(Herd) returns summarized values for each stage from each group. Note that summary functions automatically exclude outliers.

Usage

levels(x, ...)

## S4 method for signature 'Seahorse'
levels(x, blanks = TRUE, outliers = FALSE)

rates(x, ...)

## S4 method for signature 'Seahorse'
rates(x, blanks = TRUE, outliers = FALSE, normalize = TRUE)

## S4 method for signature 'Herd'
rates(x, outliers = FALSE)

summary(object, ...)

## S4 method for signature 'Seahorse'
summary(object)

## S4 method for signature 'Herd'
summary(object)

mst(x)

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

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

gst(x)

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

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

atp(x, ...)

## S4 method for signature 'Seahorse'
atp(x, format = c("table", "scatter", "bar"))

## S4 method for signature 'Herd'
atp(x, format = c("table", "scatter", "bar"))

Arguments

x	An R object. Currently there are methods for Seahorse and Herd objects.
...	Additional arguments passed to other functions.
blanks	Include blanks in output?
outliers	Include outliers in output?
normalize	Divide values by normalization factor?
object	An R object.
format	Three output options are available. For table, ATP production rates are returned in table format. For scatter, the data are formatted for an x-y scatter plot. For bar, the data return as a list of summarized data and points for a stacked bar plot.

Functions

• levels(): The O2 and pH measurements used to calculate oxygen consumption and extracellular acidification rates, respectively.

• rates(): The oxygen consumption and extracellular acidification or proton efflux rates.

• summary(): For basal, measurements, the last value of the stage is returned. For oligo and rot/ama OCR measurements, the minimum value of the stage is returned. For the ECAR/PER measurements, the maximum value of the stage is returned. For all other stages, the last value in the stage is returned for both OCR and ECAR.

• mst(): Values calculated from a mitochondrial stress assay. The spare respiratory capacity (src) is the ratio of FCCP / basal OCR after subtracting non-mitochondrial OCR (i.e., OCR following rotenone and antimycin A treatment). The coupling fraction is the proportion of basal OCR dedicated to ATP production.

• gst(): The fold increase in ECAR or PER following oligomycin.

• atp(): The ATP production rates from oxidative phosphorylation (mito) and glycolysis (glyco).

Examples

levels(sheldon)
levels(sheldon, blanks = FALSE, outliers = FALSE)

rates(sheldon)
rates(sheldon, blanks = FALSE, outliers = FALSE)
rates(herd)

summary(sheldon)
summary(herd)

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