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

Description Usage Arguments Value Examples

View source: R/cytof_preProcess.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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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

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

cytofkit documentation built on Sept. 8, 2017, 2:01 a.m.