clusterExpressionPatterns {tradeSeq} | R Documentation |
Cluster genes in clusters with similar expression patterns along the trajectory.
## 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, ...)
models |
The list of GAMs, typically the output from
|
nPoints |
The number of points to use for clustering the expression patterns. |
genes |
A numerical or character vector specifying the genes from
|
reduceMethod |
Method used before running the clustering methods.
Passed to |
nReducedDims |
Number of dimensions kept after |
minSizes |
Number of dimensions kept after |
ncores |
Number of cores to use. Passed to
|
random.seed |
Passed to |
verbose |
Passed to |
... |
Additional arguments to be passed to
|
This method adopts the RSEC
function from the clusterExperiment package to perform consensus clustering.
A list containing the scaled fitted values yhatScaled
(for
plotting) and a ClusterExperiment
object.
data(gamList, package = "tradeSeq") clusterExpressionPatterns(gamList, 200, seq_len(11))