runExprsExtract {CytoTree} | R Documentation

## Extract the expression data from a FCS file with preprocessing

### Description

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).

### Usage

    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
    )

### Arguments

`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).

### Value

A transformed expression data matrix

### Author(s)

Chen Hao

### References

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.

### Examples

    # Read fcs files
    fcs.file <- system.file("extdata/D0.FCS", package = "CytoTree")

    # Read FCS files
    exp.data <- runExprsExtract(fcs.file, showDesc = FALSE, transformMethod = "none")

[Package CytoTree version 1.4.0 Index]