runExprsExtract: Extract the expression data from a FCS file with...

In CytoTree: A Toolkit for Flow And Mass Cytometry Data

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")

CytoTree documentation built on Nov. 10, 2020, 2 a.m.