cytofkit (version 1.4.8)

cytof_exprsExtract: 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 cytofAsinh (suggest for CyTOF data), autoLgcl (suggest for FCM data), logicle (customizable) and arcsinh (customizable).

Usage

cytof_exprsExtract(fcsFile, verbose = FALSE, comp = FALSE, markers = NULL, transformMethod = c("cytofAsinh", "autoLgcl", "logicle", "arcsinh"), 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

Boolean value detecides if print the massage details of FCS loading.

comp

Either boolean value tells if do compensation (compensation matrix contained in FCS), or a compensation matrix to be applied.

markers

Selected markers for analysis, either marker names/descriptions or marker IDs.

transformMethod

Data Transformation method, including cytofAsinh (suggest for CyTOF data), autoLgcl (suggest for FCM data), logicle and arcsinh.

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 transformend expression data matrix with selected markers, row names added as filename_cellID, column mamed added as name.

Examples

d <- system.file('extdata',package='cytofkit')
fcsFile <- list.files(d,pattern='.fcs$',full=TRUE)
parameters <- list.files(d, pattern='.txt$', full=TRUE)
markers <- as.character(read.table(parameters, sep = "\t", header = TRUE)[, 1])
transformed <- cytof_exprsExtract(fcsFile, markers = markers)