Wrapper for identifying genes with significant changes with respect to one of the TSCAN pseudotime paths
runTSCANDEG(inSCE, pathIndex, useAssay = "logcounts", discardCluster = NULL)
Input SingleCellExperiment object.
Path index for which the pseudotime values should be used.
This corresponds to the terminal node of specific path from the root
node to the terminal node. Run listTSCANTerminalNodes(inSCE)
for
available options.
Character. The name of the assay to use for testing the
expression change. Should be log-normalized. Default "logcounts"
Cluster(s) which are not of use or masks other
interesting effects can be discarded. Default NULL
.
The input inSCE
with results updated in metadata
.
data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
useReducedDim = "PCA_logcounts")
#> Sat Mar 18 10:31:33 2023 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Sat Mar 18 10:31:34 2023 ... Identified 2 clusters
#> Sat Mar 18 10:31:34 2023 ... Running TSCAN to estimate pseudotime
#> Sat Mar 18 10:31:34 2023 ... Clusters involved in path index 2 are: 1, 2
#> Sat Mar 18 10:31:34 2023 ... Number of estimated paths is 1
terminalNodes <- listTSCANTerminalNodes(mouseBrainSubsetSCE)
mouseBrainSubsetSCE <- runTSCANDEG(inSCE = mouseBrainSubsetSCE,
pathIndex = terminalNodes[1])