[BioC] get parameters of estimateLogicle
Samuel [guest]
guest at bioconductor.org
Wed Feb 26 11:11:15 CET 2014
Hi,
I would to get the parameters a, w, m, t that the estimateLogicle computes. The question may be extended to how to get parameters from a transformList or a transformMap. What I would like, is a function that returns the same information as summary applied to a user defined transform.
Cheers.
> data(GvHD)
> samp <- GvHD[[1]]
> lgcl <- estimateLogicle(samp, channels = c("FL3-H", "FL4-H"))
> str(lgcl)
Formal class 'transformList' [package "flowCore"] with 2 slots
..@ transforms :List of 2
.. ..$ FL3-H:Formal class 'transformMap' [package "flowCore"] with 3 slots
.. .. .. ..@ output: chr "FL3-H"
.. .. .. ..@ input : chr "FL3-H"
.. .. .. ..@ f :function (x)
.. ..$ FL4-H:Formal class 'transformMap' [package "flowCore"] with 3 slots
.. .. .. ..@ output: chr "FL4-H"
.. .. .. ..@ input : chr "FL4-H"
.. .. .. ..@ f :function (x)
..@ transformationId: chr "defaultTransformation"
>
> lgcl <- logicleTransform(w = 0.74, t=2^18, m =4.5)
> str(lgcl)
Formal class 'transform' [package "flowCore"] with 2 slots
..@ transformationId: chr "defaultLogicleTransform"
..@ .Data :function (x)
> summary(lgcl)
$a
[1] 0
$k
transform object 'defaultLogicleTransform'
$m
[1] 4.5
$t
[1] 262144
$transformationId
[1] "defaultLogicleTransform"
$w
[1] 0.74
-- output of sessionInfo():
-
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