FlowSOM {FlowSOM} | R Documentation

## Run the FlowSOM algorithm

### Description

Method to run general FlowSOM workflow. Will scale the data and uses consensus meta-clustering by default.

### Usage

    FlowSOM(
      input,
      pattern = ".fcs",
      compensate = FALSE,
      spillover = NULL,
      transform = FALSE,
      toTransform = NULL,
      transformFunction = flowCore::logicleTransform(),
      transformList = NULL,
      scale = FALSE,
      scaled.center = TRUE,
      scaled.scale = TRUE,
      silent = TRUE,
      colsToUse = NULL,
      nClus = 10,
      maxMeta = NULL,
      importance = NULL,
      seed = NULL,
      ...
    )

### Arguments

`input` | a flowFrame, a flowSet or an array of paths to files or directories
`pattern` | if input is an array of file- or directorynames, select only files containing pattern
`compensate` | logical, does the data need to be compensated
`spillover` | spillover matrix to compensate with If NULL and compensate = TRUE, we will look for $SPILL description in fcs file.
`transform` | logical, does the data need to be transformed with a logicle transform
`toTransform` | column names or indices that need to be transformed. Will be ignored if `transformList` is given. If `NULL` and transform = `TRUE`, column names of `$SPILL` description in fcs file will be used.
`transformFunction` | Defaults to logicleTransform()
`transformList` | transformList to apply on the samples.
`scale` | logical, does the data needs to be rescaled. Default = FALSE
`scaled.center` | see `scale`
`scaled.scale` | see `scale`
`silent` | if `TRUE`, no progress updates will be printed
`colsToUse` | Markers, channels or indices to use for building the SOM. Default (NULL) is all the columns used to build the FlowSOM object.
`nClus` | Exact number of clusters for meta-clustering. Ignored if maxMeta is specified. Default = 10.
`maxMeta` | Maximum number of clusters to try out for meta-clustering. If `NULL` (default), only one option will be computed (`nClus`).
`importance` | array with numeric values. Parameters will be scaled according to importance
`seed` | Set a seed for reproducible results
`...` | options to pass on to the SOM function (xdim, ydim, rlen, mst, alpha, radius, init, distf)

### Value

A `list` with two items: the first is the flowSOM object containing all information (see the vignette for more detailed information about this object), the second is the metaclustering of the nodes of the grid. This is a wrapper function for `ReadInput`, `BuildSOM`, `BuildMST` and `MetaClustering`. Executing them separately may provide more options.

### See Also

`scale`, `ReadInput`, `BuildSOM`, `BuildMST`, `MetaClustering`

### Examples

    # Read from file
    fileName <- system.file("extdata", "68983.fcs", package = "FlowSOM")
    flowSOM.res <- FlowSOM(fileName, compensate = TRUE, transform = TRUE,
                          scale = TRUE, colsToUse = c(9, 12, 14:18), nClus = 10)
    # Or read from flowFrame object
    ff <- flowCore::read.FCS(fileName)
    ff <- flowCore::compensate(ff, flowCore::keyword(ff)[["SPILL"]])
    ff <- flowCore::transform(ff,
             flowCore::transformList(colnames(flowCore::keyword(ff)[["SPILL"]]),
                                    flowCore::logicleTransform()))
    flowSOM.res <- FlowSOM(ff,
                           scale = TRUE,
                           colsToUse = c(9, 12, 14:18),
                           nClus = 10)

    # Plot results
    PlotStars(flowSOM.res,
              backgroundValues = flowSOM.res$metaclustering)

    # Get metaclustering per cell
    flowSOM.clustering <- GetMetaclusters(flowSOM.res)

[Package FlowSOM version 2.2.0 Index]