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")
#> Tue Jun 28 22:07:36 2022 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Tue Jun 28 22:07:36 2022 ... Identified 2 clusters
#> Tue Jun 28 22:07:36 2022 ... Running TSCAN to estimate pseudotime
#> Tue Jun 28 22:07:37 2022 ... Clusters involved in path index 2 are: 1, 2
#> Tue Jun 28 22:07:37 2022 ... Number of estimated paths is 1
terminalNodes <- listTSCANTerminalNodes(mouseBrainSubsetSCE)
mouseBrainSubsetSCE <- runTSCANDEG(inSCE = mouseBrainSubsetSCE,
pathIndex = terminalNodes[1])