normalization-class {flowCore} | R Documentation |
Class and methods to normalize a a flowSet
using a potentially
complex normalization function.
normalization(parameters, normalizationId="defaultNormalization", normFunction, arguments=list()) normalize(data, x,...)
parameters |
Character vector of parameter names. |
normalizationId |
The identifier for the normalization object. |
x |
An object of class |
normFunction |
The normalization function |
arguments |
The list of additional arguments to
|
data |
The |
... |
other arguments:
see |
Data normalization of a flowSet
is a rather fuzzy concept and
the class mainly exists for method dispatch in the workflow
tools. The idea is to have a rather general function that takes a
flowSet
and a list of parameter names as input and applies any
kind of normalization to the respective data columns. The output of
the function has to be a flowSet
again. Although we don't
formally check for it, the dimensions of the input and of the output
set should remain the same. Additional arguments may be passed to the
normalization function via the arguments
list. Internally we
evaluate the function using do.call
and one should check
its documentation for details.
Currently, the most prominent example for a normalization function is
warping, as provided by the flowStats
package.
A normalization
object for the constructor.
A flowSet
for the normalize
methods.
Objects should be created using the constructor
normalization()
. See the Usage
and Arguments
sections for details.
parameters
:Object of class "character"
. The
flow parameters that are supposed to be normalized by the
normalization function.
normalizationId
:Object of class "character"
. An
identifier for the object.
normFunction
:Object of class "function"
The
normalization function. It has to take two mandatory arguments:
x
, the flowSet
, and parameters
, a character
of parameter names that are to be normalized by the
function. Additional arguments have to be passed in via
arguments
.
arguments
:Object of class "list"
A names list
of additional arguments. Can be NULL
.
signature(wf = "workFlow", action =
"normalization")
: The constructor for the workFlow.
signature(object = "normalization", value
= "character")
: Set method for the identifier slot.
signature(object = "normalization")
: Get
method for the identifier slot.
signature(data = "flowSet", x =
"normalization")
: Apply a normalization to a flowSet
.
signature(object = "normalization")
: The
more generic constructor.
F. Hahne