blanks: Blanks accessors for 'seahorse' S4 objects

In wmoldham/seahorse: Analyze Seahorse Bioenergetic Data

Blanks accessors for seahorse S4 objects

Description

Blank values are essential for accurate calculations of oxygen consumption (OCR) and extracellular acidification (ECAR) rates. Wells removed from blanks are added to the list of experimental outliers.

Usage

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

## S4 replacement method for signature 'Seahorse'
blanks(x, action = c("remove", "reset", "replace", "add", "subtract")) <- value

Arguments

x	A Seahorse object.
action	Indicates how replacement values modify the existing values: action     description remove     set all values to NA reset     assign blanks based on the original data file replace     completely replace blanks with new values add     add new blank wells subtract     remove blank wells
value	A data frame with two columns named rate and well. The rate columns should contain either OCR or ECAR. The well column identifies the blank wells formatted as "A01". Changing blank wells automatically recalculates OCR and ECAR values. For the "reset" and "remove" actions, the assigned value is ignored, but use NA.

Value

blanks(x) returns a data frame of wells used as blanks for OCR and ECAR calculations.

Examples

blanks(sheldon)
blanks(sheldon, "replace") <- list(OCR = "A01")
blanks(sheldon)
blanks(sheldon, "reset") <- NA
blanks(sheldon)

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