clusterExpressionPatterns: Cluster gene expression patterns.

clusterExpressionPatternsR 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)

statOmics/tradeSeq documentation built on Jan. 19, 2024, 8:26 p.m.