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

In haoeric/cytofkit_devel: cytofkit: an integrated mass cytometry data analysis pipeline

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, markers = NULL,
  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	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 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 transformend expression data matrix with selected markers, row names added as filename_cellID, column mamed added as name<desc>.

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)

haoeric/cytofkit_devel documentation built on May 17, 2019, 2:29 p.m.