runExprsExtract: Extract the expression data from a FCS file with...
In JhuangLab/flowSpy: A Toolkit for Flow And Mass Cytometry Data

Description Usage Arguments Value Author(s) References Examples

Extract the FCS expresssion data with preprocessing of compensation (for FCM data only) and transformation. Transformtion methods includes autoLgcl, cytofAsinh, logicle (customizable) and arcsinh (customizable).

runExprsExtract(
  fcsFile,
  verbose = FALSE,
  comp = FALSE,
  transformMethod = c("autoLgcl", "cytofAsinh", "logicle", "arcsinh", "logAbs", "none"),
  scaleTo = NULL,
  showDesc = TRUE,
  keepRaw = TRUE,
  q = 0.05,
  l_w = 0.1,
  l_t = 4000,
  l_m = 4.5,
  l_a = 0,
  a_a = 1,
  a_b = 1,
  a_c = 0
)

`fcsFile`	The name of the FCS file.
`verbose`	If `TRUE`, print the message details of FCS loading.
`comp`	If `TRUE`, does compensation by compensation matrix contained in FCS. Agrument also accepts a compensation matrix to be applied. Otherwise `FALSE`.
`transformMethod`	Data Transformation method, including `autoLgcl`, `cytofAsinh`, `logicle` and `arcsinh`, or `none` to avoid transformation.
`scaleTo`	Scale the expression to a specified range c(a, b), default is NULL.
`showDesc`	logical. Whether to show `desc` name in the output matrix.
`keepRaw`	logical. Whether to keep raw data for FSC and SSC.
`q`	Quantile of negative values removed for auto w estimation, default is 0.05, parameter for autoLgcl transformation.
`l_w`	Linearization width in asymptotic decades, parameter for logicle transformation.
`l_t`	Top of the scale data value, parameter for logicle transformation.
`l_m`	Full width of the transformed display in asymptotic decades, parameter for logicle transformation.
`l_a`	Additional negative range to be included in the display in asymptotic decades, parameter for logicle transformation.
`a_a`	Positive double that corresponds to the base of the arcsinh transformation, `arcsinh` = asinh(a + b * x) + c).
`a_b`	Positive double that corresponds to a scale factor of the arcsinh transformation, `arcsinh` = asinh(a + b * x) + c).
`a_c`	Positive double that corresponds to another scale factor of the arcsinh transformation, `arcsinh` = asinh(a + b * x) + c).

A transformed expression data matrix

Chen Hao

Hao Chen, Mai Chan Lau, Michael Thomas Wong, Evan W. Newell, Michael Poidinger, Jinmiao Chen. Cytofkit: A Bioconductor Package for an Integrated Mass Cytometry Data Analysis Pipeline. PLoS Comput Biol, 2016.

if (FALSE) {
# See vignette tutorials for more information
vignette(package = "flowSpy")
vignette("Quick_start", package = "flowSpy")

  # Path to your FCS files
  fcs.path <- "flowSpy-dataset/FCS/usecase1/"
  fcs.file <- paste0(fcs.path, "FR-FCM-ZY9R-Bone_Marrow_cytof.fcs")

  # Read FCS files
  exp.data <- runExprsExtract(fcs.file, showDesc = FALSE, transformMethod = "autoLgcl")
}