cytof_exprsExtract {cytofkit} | 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

    cytof_exprsExtract(fcsFile, verbose = FALSE, comp = FALSE,
      transformMethod = c("autoLgcl", "cytofAsinh", "logicle", "arcsinh", "none"),
      scaleTo = NULL, 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.
`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, row names added as `filename_cellID`, column names added as `name<desc>`.

### Examples

    d <- system.file('extdata',package='cytofkit')
    fcsFile <- list.files(d,pattern='.fcs$',full=TRUE)
    transformed <- cytof_exprsExtract(fcsFile)

[Package cytofkit version 1.12.0 Index]