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

Description Usage Arguments Value Author(s) References Examples

View source: R/preprocessing.R

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

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runExprsExtract(
  fcsFile,
  verbose = FALSE,
  comp = FALSE,
  transformMethod = c("autoLgcl", "cytofAsinh", "logicle", "arcsinh", "logAbs", "none"),
  scaleTo = NULL,
  showDesc = 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.

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

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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")
}

flowSpy documentation built on Nov. 8, 2020, 6:53 p.m.