flowSet2LongDf {flowSpecs} | R Documentation

## Convert a flowSet to one long dataframe with all identifiers as separate #columns.

### Description

This function is mainly used for compatibility with matrix-based clustering algorithms, such as depeche in the DepecheR package.

### Usage

    flowSet2LongDf(flowObj, idInfo)

### Arguments

`flowObj` | The flowSet or flowFrame to be converted to a dataframe.
`idInfo` | A list of any number of characteristics that can be derived from the file names. For each entry, a gsub specification of where to find the information in the file name should be added, such as id=""..._|..."".

### Value

A long data frame with one column per PMT/APD (or fluorochrome, depending on the state of the imported files), one for the acquisition date (for fcs files) and one colum for each specified slot above. If no gsub-pattern is provided, only a single column with the full file name will be used to separate the observations from each file.

### See Also

`depeche`

### Examples

    #' # Load uncompensated data
    data(fullPanel)

    # Load the spectral unmixing matrix generated with controls from the same
    # experiment. These can be generated using the specMatCalc function.
    data(specMat)

    # Now unmix
    fullPanelUnmix <- specUnmix(fullPanel, specMat)

    # Transform all fluorescent channels
    fullPanelTrans <- arcTrans(fullPanelUnmix,
        transNames = colnames(fullPanelUnmix)[6:18])

    # This function is primarily meant to be used with flowSets.
    # If we had only one flowFrame, we could just extract the data by
    # the use of the flowCore function exprs(), so we will convert the data to a
    # flowSet now.
    library(flowCore)
    fullPanelFs <- flowSet(fullPanelTrans)

    # Before converting to a dataframe it is important to get an idea of the
    # structure of the names, to be able to extract meaningful parts of the name.
    # Here, we have an exceptional case again, as the flowSet has just been
    # created, so there is actually no meaningful name of the flowFrame inside
    # it. So for example reasons, we will give it one now:
    sampleNames(fullPanelFs) <- "PBMC_full_panel_d1.fcs"

    # And now, we generate the dataframe:
    fullPanelDf <- flowSet2LongDf(fullPanelFs, idInfo =
                                     list("Tissue" = "|_full_panel_..\\.fcs",
                                         "Donor" = "...._full_panel_|\\.fcs"))
    # This is the result
    str(fullPanelDf)

[Package flowSpecs version 1.0.2 Index]