preprocessing {MetaCyto} | R Documentation

## Preprocess fcs files from a single experiment

### Description

A function that preprocesses fcs files from a single experiment.

### Usage

    preprocessing(fcsFiles, assay = c("FCM", "CyTOF"), b = 1/200,
      fileSampleSize = 5000, compFiles = NULL,
      excludeTransformParameters = c("FSC-A", "FSC-W", "FSC-H", "Time",
      "Cell_length"))

### Arguments

`fcsFiles` | A vector specifying the location of all fcs files.
`assay` | Either "FCM" or "CyTOF" to indicate the type of cytometry data.
`b` | A positive number used to specify the arcsinh transformation. f(x) = asinh (b*x) where x is the original value and f(x) is the value after transformation. The suggested value is 1/150 for flow cytometry (FCM) data and 1/8 for CyTOF data. If b = 0, the transformation is skipped.
`fileSampleSize` | An integer specifying the number of events sampled from each fcs file. If NULL, all the events will be pre-processed and wrote out to the new fcs files.
`compFiles` | A vector specifying the paths of user supplied compensation matrix for each fcs file. The matrix must be stored in csv files.
`excludeTransformParameters` | A vector specifying the name of parameters not to be transformed (left at linear scale).

### Value

Returns a flowFrame object containing the preprocessed cytometry data. Cells from different fcs files are combined into one flow frame. A new parameter, sample_id, is introduced to indicate the origin of each cell.

### Examples

    # Find fcs files
    files=system.file("extdata","SDY420/ResultFiles/CyTOF_result",
                      package="MetaCyto")
    files=list.files(files,pattern="fcs$",full.names=TRUE)
    # Preprocess
    fcs = preprocessing(fcsFiles=files,assay ="CyTOF",b=1/8)

[Package MetaCyto version 1.4.1 Index]