compensatedParameter-class {flowCore} | R Documentation |
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 can be created by calls of the form
compensatedParameter(parameters,spillRefId,transformationId,searchEnv)
.
.Data
:"function"
~~ parameters
:"character"
-flow parameters to
be compensated spillRefId
:"character"
-name of the
compensation object (The compensation object contains the spillover Matrix) searchEnv
:"environment"
-environment in
which the compensation object is defined transformationId
:"character"
-unique Id to
reference the compensatedParameter object
Class "transform"
, directly.
Class "transformation"
, by class "transform", distance 2.
Class "characterOrTransformation"
, by class "transform", distance 3.
No methods defined with class "compensatedParameter" in the signature.
The transformation object can be evaluated using the eval method by passing the data frame as an argument.The transformed parameters are returned as a matrix with a single column. (See example below)
Gopalakrishnan N,F.Hahne
~~
compensation
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]]))