cytof_exprsMerge {cytofkit} | R Documentation

## Merge the expression matrix from multiple FCS files with preprocessing

### 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

    cytof_exprsMerge(fcsFiles, comp = FALSE, transformMethod = c("autoLgcl",
      "cytofAsinh", "logicle", "arcsinh", "none"), scaleTo = NULL,
      mergeMethod = c("ceil", "all", "fixed", "min"), fixedNum = 10000,
      sampleSeed = 123, ...)

### 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.
`sampleSeed` | A sampling seed for reproducible expression matrix merging.
`...` | Other arguments passed to `cytof_exprsExtract`

### Value

A matrix containing the merged expression data, with selected markers, row names added as `filename_cellID`, column names added as `name<desc>`.

### See Also

`cytof_exprsExtract`

### Examples

    d<-system.file('extdata',package='cytofkit')
    fcsFiles <- list.files(d,pattern='.fcs$',full=TRUE)
    merged <- cytof_exprsMerge(fcsFiles)

[Package cytofkit version 1.12.0 Index]