import.FCS: Importation of cell profiles from one or several FCS files
In tchitchek-lab/CytoCompare: Computational comparisons of cytometry profiles

Description Usage Arguments Details Value

Imports one or several cell profiles from a FCS file or from a set of FCS files into a CELL object.

import.FCS(path, exclude = NULL, trans = "arcsinh",
  trans.para = switch(trans, arcsinh = list(arcsinh.scale = 5), log =
  list(log.shift = "auto", log.base = 10), none = NULL),
  trans.exclude = "cluster", rescale = FALSE,
  rescale.quantiles = c(0, 1))

`path`	a character vector indicating the location to a FCS file or to a set of FCS files
`exclude`	a character vector containing the marker names to be excluded in the import procedure
`trans`	a character specifying the name of a transformation function to apply on the marker expression intensities. Possible functions are "arcsinh" for arc sin hyperbolic transformation (default), "log" for logarithmic transformation, or "none" for no transformation
`trans.para`	a named list containing parameters for the transformation. Please refer to the details section for more details
`trans.exclude`	a character vector containing the marker names for which no transformation must be applied on (including the rescaling transformation)
`rescale`	a logical specifying if marker expression intensities must be rescale between 0 and 1
`rescale.quantiles`	a numeric vector of two values specifying the quantiles of the marker expression intensities used to rescale

If a set of files is specified, then the files are merged in the import procedure.

Several transformations can be applied on the expression marker intensities via the 'trans' parameter:

The transformation functions can be parametrized using the named list 'trans.para'. The scale (cofactor) of the arcsinh transformation function can be parametrized using the 'arcsinh.scale' value. The shift of the log transformation function can be parametrized using the 'log.shift' value and the base of the log transformation function can be parametrized using the 'log.base' value. The 'log.shift' allows the value "auto" which automatically identify the log shift avoiding to apply log transformations on negative values.

The 'rescale' parameter can be used to rescale the marker expression intensities from 0 to 1 (with respect to the distribution proportion). The rescaling can be performed based on minimal and maximal expression values or based on specified quantiles using the 'rescale.quantiles' parameter. This strategy is especialy usefull when comparing cell or cell cluster profiles obtained from different experimental/staining conditions.

a S4 object of class CELL

tchitchek-lab/CytoCompare documentation built on May 31, 2019, 7:29 a.m.