Run TSCAN to obtain pseudotime values for cells

Source: R/runTSCAN.R

Wrapper for obtaining a pseudotime ordering of the cells by projecting them onto the minimum spanning tree (MST)

runTSCAN(
  inSCE,
  useReducedDim = "PCA",
  cluster = NULL,
  starter = NULL,
  seed = 12345
)

Arguments

inSCE

Input SingleCellExperiment object.

useReducedDim

Character. A low-dimension representation in reducedDims, will be used for both clustering if cluster not specified and MST construction. Default "PCA".

cluster

Grouping for each cell in inSCE. A vector with equal length to the number of the cells in inSCE, or a single character for retriving colData variable. Default NULL, will run runScranSNN to obtain.

starter

Character. Specifies the starting node from which to compute the pseudotime. Default NULL, will select an arbitrary node.

seed

An integer. Random seed for clustering if cluster is not specified. Default 12345.

Value

The input inSCE object with pseudotime ordering of the cells along the paths and the cluster label stored in colData, and other unstructured information in metadata.

Author

Nida Pervaiz

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                useReducedDim = "PCA_logcounts")
#> Wed Jan 10 17:49:03 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Wed Jan 10 17:49:04 2024 ...   Identified 2 clusters
#> Wed Jan 10 17:49:04 2024 ... Running TSCAN to estimate pseudotime
#> Wed Jan 10 17:49:04 2024 ...   Clusters involved in path index 2 are: 1, 2
#> Wed Jan 10 17:49:04 2024 ...   Number of estimated paths is 1