Wrapper for obtaining a pseudotime ordering of the cells by projecting them onto the minimum spanning tree (MST)
runTSCAN(inSCE, useReducedDim = "PCA", cluster = NULL, seed = 12345)Input SingleCellExperiment object.
Character. A low-dimension representation in
reducedDims, will be used for both clustering if cluster not
specified and MST construction. Default "PCA".
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.
An integer. Random seed for clustering if cluster is not
specified. Default 12345.
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.
data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
useReducedDim = "PCA_logcounts")
#> Sat Mar 18 10:31:31 2023 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Sat Mar 18 10:31:32 2023 ... Identified 2 clusters
#> Sat Mar 18 10:31:32 2023 ... Running TSCAN to estimate pseudotime
#> Sat Mar 18 10:31:32 2023 ... Clusters involved in path index 2 are: 1, 2
#> Sat Mar 18 10:31:32 2023 ... Number of estimated paths is 1