FCSTransTransform: Computes a transform using the 'iplogicle' function
In flowCore: flowCore: Basic structures for flow cytometry data

Description Usage Arguments Details Author(s) References See Also Examples

Transforms FCS data using the iplogicle function from FCSTrans by Quian et al. The core functionality of FCSTrans has been imported to produce transformed FCS data rescaled and truncated as produced by FCSTrans. The w parameter is estimated by iplogicle automatically, then makes a call to iplogicore which in turn uses the logicle transform code of Wayne Moore.

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FCSTransTransform(transformationId = "defaultFCSTransTransform", 
                  channelrange = 2^18, channeldecade = 4.5, 
                  range = 4096, cutoff = -111, w = NULL, rescale = TRUE)

`transformationId`	A name to assign to the transformation. Used by the transform/filter routines.
`channelrange`	is the range of the data. By default, 2^18 = 262144.
`channeldecade`	is the number of logarithmic decades. By default, it is set to 4.5.
`range`	the target resolution. The default value is 2^12 = 4096.
`cutoff`	a threshold below which the logicle transformation maps values to 0.
`w`	the logicle width. This is estimated by `iplogicle` by default. Details can be found in the Supplementary File from Quian et al.
`rescale`	logical parameter whether or not the data should be rescaled to the number of channels specified in `range`. By default, the value is `TRUE` but can be set to FALSE if you want to work on the transformed scale.

For the details of the FCSTrans transformation, we recommend the excellent Supplementary File that accompanies Quian et al. (2012): http://onlinelibrary.wiley.com/doi/10.1002/cyto.a.22037/suppinfo

Wayne Moore, N Gopalakrishnan

Y Quian, Y Liu, J Campbell, E Thompson, YM Kong, RH Scheuermann; FCSTrans: An open source software system for FCS file conversion and data transformation. Cytometry A, 2012

inverseLogicleTransform, estimateLogicle , logicleTransform

data(GvHD)
samp <- GvHD[[1]] 
## User defined logicle function
lgcl <- transformList(c('FL1-H', 'FL2-H'), FCSTransTransform())
after <- transform(samp, lgcl)