depeche {DepecheR} | R Documentation

## Perform optimization and penalized K-means clustering

### Description

This is the central function of the package. As input, only a dataset is required. It starts by performing optimizations and then performs clustering based on the values identified in the optimization step.

### Usage

    depeche(
      inDataFrame,
      samplingSubset = seq_len(nrow(inDataFrame)),
      penalties = 2^seq(0, 5, by = 0.5),
      sampleSize = "default",
      selectionSampleSize = "default",
      k = 30,
      minARIImprovement = 0.01,
      optimARI = 0.95,
      maxIter = 100,
      log2Off = FALSE,
      center = "default",
      scale = TRUE,
      nCores = "default",
      plotDir = ".",
      createOutput = TRUE
    )

### Arguments

`inDataFrame` | A dataframe or matrix with the data that will be used to create the clustering. Cytometry data should be transformed using biexponential, arcsinh transformation or similar, and day-to-day normalizations should to be performed for all data if not all data has been acquired on the same run. Scaling, etc, is on the other hand performed within the function.
`samplingSubset` | If the dataset is made up of an unequal number of cells from multiple individuals, it might be wise to pre-define a subset of the rows, which includes equal or near-equal numbers of cells from each individual, to avoid a few outliers to dominate the analysis. This can be done here. Should be a vector of row numbers in the inDataFrame.
`penalties` | This argument decides whether a single penalty will be used for clustering, or if multiple penalties will be evaluated to identify the optimal one. A single value, a vector of values, or possibly a list of two vectors, if dual clustering is performed can be given here. The suggested default values are empirically defined and might not be optimal for a specific dataset, but the algorithm will warn if the most optimal values are on the borders of the range. Note that when the penalty is 0, there is no penalization, which means that the algorithm runs standard K-means clustering.
`sampleSize` | This controls what fraction of the dataset that will be used to run the penalty optimization. 'default' results in the full file in files up to 10000 events. In cases where the sampleSize argument is larger than 10000, default leads to the generation of a random subset to the same size also for the selectionSampleSize. A user specified number is also accepted.
`selectionSampleSize` | The size of the dataset used to find the optimal solution out of the many generated by the penalty optimization at each sample size. 'default' results in the full file in files up to 10000 events. In cases where the sampleSize argument is larger than 10000, default leads to the generation of a random subset to the same size also for the selectionSampleSize. A user specified number is also accepted.
`k` | Number of initial cluster centers. The higher the number, the greater the precision of the clustering, but the computing time also increases linearly with the number of starting points. Default is 30. If penalties=0, k-means clustering with k clusters will be performed.
`minARIImprovement` | This is the stop criterion for the penalty optimization algorithm: the more iterations that are run, the smaller will the improvement of the corrected Rand index be, and this sets the threshold when the inner iterations stop. Defaults to 0.01.
`optimARI` | Above this level of ARI, all solutions are considered equally valid, and the median solution is selected among them.
`maxIter` | The maximal number of iterations that are performed in the penalty optimization.
`log2Off` | If the automatic detection for high kurtosis, and followingly, the log2 transformation, should be turned off.
`center` | If centering should be performed. Alternatives are 'default', 'mean', 'peak', FALSE and a vector of numbers with the same length as the number of columns in the inDataFrame. 'peak' results in centering around the highest peak in the data, which is useful in most cytometry situations. 'mean' results in mean centering. 'default' gives different results depending on the data: datasets with 100+ variables are mean centered, and otherwise, peak centering is used. If a numeric vector is provided, it is used to center the values to the numbers. This is preferable to pre-centering the data and using the FALSE command, as it will lead to better internal visualization procedures, etc. FALSE results in no centering, mainly for testing purposes.
`scale` | If scaling should be performed. If TRUE, the dataset will be divided by the combined standard deviation of the whole dataset. If a number is provided, the dataset is divided by this number. This scaling procedure makes the default penalties fit most datasets with some precision.
`nCores` | If multiCore is TRUE, then this sets the number of parallel processes. The default is currently 87.5 percent with a cap on 10 cores, as no speed increase is generally seen above 10 cores for normal computers.
`plotDir` | Where should the diagnostic plots be printed?
`createOutput` | For testing purposes. Defaults to TRUE. If FALSE, no plots are generated.

### Value

A nested list:

clusterVector

  A vector with the same length as number of rows in the inDataFrame, where the cluster identity of each observation is noted.

clusterCenters

  A matrix containing information about where the centers are in all the variables that contributed to creating the cluster with the given penalty term. An exact zero here indicates that the variable in question was sparsed out for that cluster. If a variable did not contribute to the separation of any cluster, it will not be present here.

essenceElementList

  A per-cluster list of the items that were used to separate that cluster from the rest, i.e. the items that survived the penalty.

penaltyOptList

  A list of two dataframes:

  penaltyOpt.df

    A one row dataframe with the settings for the optimal penalty.

  meanOptimDf

    A dataframe with the information about the results with all tested penalty values.

logCenterScale

  The values used to center and scale the data and information on if the data was log transformed. This information is used internally in dAllocate.

### Examples

    # Load some data
    data(testData)

    # Here a run with the standard settings
    ## Not run:
    testDataDepecheResult <- depeche(testData[, 2:15])

    # Look at the result
    str(testDataDepecheResult)

    ## End(Not run)

[Package DepecheR version 1.8.0 Index]