clusterExpressionPatterns {tradeSeq} | R Documentation

## Cluster gene expression patterns.

### Description

Cluster genes in clusters that have similar expression patterns along all lineages in the trajectory. By default, this function uses the `clusterExperiment` package to do the clustering. If another clustering method is of interest, one can extract fitted values to use for clustering, see details in the vignette.

### Usage

    ## S4 method for signature 'SingleCellExperiment'
    clusterExpressionPatterns(
      models,
      nPoints,
      genes,
      reduceMethod = "PCA",
      nReducedDims = 10,
      minSizes = 6,
      ncores = 1,
      random.seed = 176201,
      verbose = TRUE,
      ...
    )

    ## S4 method for signature 'list'
    clusterExpressionPatterns(
      models,
      nPoints,
      genes,
      reduceMethod = "PCA",
      nReducedDims = 10,
      minSizes = 6,
      ncores = 1,
      random.seed = 176201,
      verbose = TRUE,
      ...
    )

### Arguments

`models` | The fitted GAMs, typically the output from `fitGAM`.
`nPoints` | The number of points to use for clustering the expression patterns.
`genes` | A numerical or character vector specifying the genes from `models` that should be clustered.
`reduceMethod` | Dimensionality reduction method used before running the clustering methods. Passed to `RSEC`. Defaults to PCA.
`nReducedDims` | Number of dimensions kept after `reduceMethod`. Passed to `RSEC`.
`minSizes` | Minimum size of clusters. Passed to `RSEC`.
`ncores` | Number of cores to use. Passed to `RSEC`
`random.seed` | Passed to `RSEC`
`verbose` | Passed to `RSEC`
`...` | Additional arguments to be passed to `RSEC`.

### Details

This method adopts the `RSEC` function from the clusterExperiment package to perform consensus clustering.

### Value

A list containing the scaled fitted values `yhatScaled`(for plotting) and a `clusterExperiment` object, containing the clustering results.

### Examples

    ## Not run:
    data(gamList, package = "tradeSeq")
    clusterExpressionPatterns(models = gamList, nPoints = 200, genes = seq_len(11),
                              verbose = FALSE)

    ## End(Not run)

[Package tradeSeq version 1.8.0 Index]