FCSTransTransform {flowCore} | R Documentation |
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.
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
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 |
rescale |
logical parameter whether or not the data should be
rescaled to the number of channels specified in |
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)