analyze: Analysis functions for Seahorse rate data
In wmoldham/seahorse: Analyze Seahorse Bioenergetic Data

analyze

R Documentation

Analysis functions for Seahorse rate data

Description

These functions operate on a rates data.frame from a Seahorse object to return summary values from various experimental designs including mitochondrial stress tests, glycolytic stress tests, and ATP production rates. These analyses are automatically performed during the creation of a Seahorse object, but these functions are exposed to the user to facilitate finer-grained analyses.

Usage

summarize_rates(x, remove_outliers = FALSE)

summarize_mst(x, remove_outliers = TRUE)

summarize_gst(x, remove_outliers = TRUE)

summarize_atp(x, bf, cf, remove_outliers = TRUE)

Arguments

`x`	A data.frame returned by `rates()`.
`remove_outliers`	Should outliers based on median absolutely deviation be removed?
`bf`	The buffer factor of the assay medium.
`cf`	The carbon dioxide correction factor.

Functions

summarize_rates(): Calculates summary values for each interval of a Seahorse object. For basal, the last measurement in the interval is returned. For oligo and rot/ama, the lowest OCR and highest ECAR values are returned. For fccp, the highest OCR and ECAR values are returned. For any other interval, the value of the last measurement in the interval is returned.
summarize_mst(): Calculates the spare respiratory capacity (src) and coupling efficiency (coupling) from a mitochondrial stress test. This test requires stages labeled basal, oligo, fccp, and rot/ama. Both values are expressed as the fold change relative to the basal OCR after subtracting non-mitochondrial OCR.
summarize_gst(): Calculates the results of a glycolytic stress test. This test requires stages labeled basal and oligo. The gst value is the fold increase in ECAR or PER following oligomycin treatment.
summarize_atp(): Calculates the mitochondrial and glycolytic ATP production rates. This test requires stages labeled basal, oligo, and rot/ama. In addition, the assay medium buffer factor (bf) and carbon dioxide correction factor (cf) must also be provided.