runExprsExtract {CytoTree} | R Documentation |
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).
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 )
fcsFile |
The name of the FCS file. |
verbose |
If |
comp |
If |
transformMethod |
Data Transformation method, including |
scaleTo |
Scale the expression to a specified range c(a, b), default is NULL. |
showDesc |
logical. Whether to show |
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, |
a_b |
Positive double that corresponds to a scale factor of the
arcsinh transformation, |
a_c |
Positive double that corresponds to another scale factor
of the arcsinh transformation, |
A transformed expression data matrix
Chen Hao
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.
# Read fcs files fcs.file <- system.file("extdata/D0.FCS", package = "CytoTree") # Read FCS files exp.data <- runExprsExtract(fcs.file, showDesc = FALSE, transformMethod = "none")