runExprsMerge: Merge the expression matrix from multiple FCS files with...
In JhuangLab/CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description Usage Arguments Value Author(s) References See Also Examples

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 `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.
`mergeMethod`	Merge method for mutiple FCS expression data. cells can be combined using one of the four different methods including `ceil`, `all`, `min`, `fixed`. The default option is `ceil`, up to a fixed number (specified by `fixedNum`) of cells are sampled without replacement from each fcs file and combined for analysis. `all`: all cells from each fcs file are combined for analysis. `min`: The minimum number of cells among all the selected fcs files are sampled from each fcs file and combined for analysis. `fixed`: a fixed num (specified by fixedNum) of cells are sampled (with replacement when the total number of cell is less than fixedNum) from each fcs file and combined for analysis.
`fixedNum`	The fixed number of cells to be extracted from each FCS file.
`...`	Other arguments passed to `runExprsExtract`

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.

runExprsExtract

# 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")