runExprsMerge {CytoTree} | R Documentation |
Apply preprocessing on each FCS file including compensation
(for FCM data only) and transformation with selected markers, then expression
matrix are extracted and merged using one of the methods, all
,
min
, fixed
or ceil
runExprsMerge( fcsFiles, comp = FALSE, transformMethod = c("autoLgcl", "cytofAsinh", "logicle", "arcsinh", "logAbs", "none"), scaleTo = NULL, mergeMethod = c("ceil", "all", "fixed", "min"), fixedNum = 2000, ... )
fcsFiles |
A vector of FCS file names. |
comp |
If |
transformMethod |
Data Transformation method, including |
scaleTo |
Scale the expression to a specified range c(a, b), default is NULL. |
mergeMethod |
Merge method for mutiple FCS expression data. cells can be
combined using one of the four different methods including |
fixedNum |
The fixed number of cells to be extracted from each FCS file. |
... |
Other arguments passed to |
A matrix containing the merged expression data, with selected markers.
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.path <- system.file("extdata", package = "CytoTree") fcs.files <- list.files(fcs.path, pattern = '.FCS$', full = TRUE) fcs.data <- runExprsMerge(fcs.files, comp = FALSE, transformMethod = "none")