runExprsMerge: Merge the expression matrix from multiple FCS files with...

In CytoTree: A Toolkit for Flow And Mass Cytometry Data

Description

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

Usage

runExprsMerge(
  fcsFiles,
  comp = FALSE,
  transformMethod = c("autoLgcl", "cytofAsinh", "logicle", "arcsinh", "logAbs", "none"),
  scaleTo = NULL,
  mergeMethod = c("ceil", "all", "fixed", "min"),
  fixedNum = 2000,
  ...
)

Arguments

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

Value

A matrix containing the merged expression data, with selected markers.

Author(s)

Chen Hao

References

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.

See Also

runExprsExtract

Examples

# 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")

CytoTree documentation built on Nov. 10, 2020, 2 a.m.