flowCore (version 1.38.2)

compensatedParameter-class: Class "compensatedParameter"

Description

Emission spectral overlap can be corrected by subtracting the the amount of spectral overlap from the total detected signals. This compensation process can be described by using spillover matrices.

compensatedParameter objects allow for compensation of specific parameters the user is interested in by creating compensatedParameter objects and evaluating them.This allows for use of compensatedParameter in gate definitions.

Objects from the Class

Objects can be created by calls of the form compensatedParameter(parameters,spillRefId,transformationId,searchEnv).

Slots

.Data:

Object of class "function" ~~

parameters:

Object of class "character" -flow parameters to be compensated

spillRefId:

Object of class "character" -name of the compensation object (The compensation object contains the spillover Matrix)

searchEnv:

Object of class "environment" -environment in which the compensation object is defined

transformationId:

Object of class "character" -unique Id to reference the compensatedParameter object

Extends

Class "transform", directly. Class "transformation", by class "transform", distance 2. Class "characterOrTransformation", by class "transform", distance 3.

Methods

No methods defined with class "compensatedParameter" in the signature.

References

~~

See Also

compensation

Examples

samp   <- read.flowSet(path=system.file("extdata", "compdata", "data", package="flowCore"))
cfile <- system.file("extdata","compdata","compmatrix", package="flowCore")
comp.mat <- read.table(cfile, header=TRUE, skip=2, check.names = FALSE)
comp.mat

## create a compensation object 
comp <- compensation(comp.mat,compensationId="comp1")
## create a compensated parameter object 
cPar1<-compensatedParameter(c("FL1-H","FL3-H"),"comp",searchEnv=.GlobalEnv)
compOut<-eval(cPar1)(exprs(samp[[1]]))