getTSCANResults accessor function

Source: R/runTSCAN.R

SCTK allows user to access all TSCAN related results with "getTSCANResults". See details.

getTSCANResults(x, analysisName = NULL, pathName = NULL)

# S4 method for class 'SingleCellExperiment'
getTSCANResults(x, analysisName = NULL, pathName = NULL)

getTSCANResults(x, analysisName, pathName = NULL) <- value

# S4 method for class 'SingleCellExperiment'
getTSCANResults(x, analysisName, pathName = NULL) <- value

listTSCANResults(x)

# S4 method for class 'SingleCellExperiment'
listTSCANResults(x)

listTSCANTerminalNodes(x)

# S4 method for class 'SingleCellExperiment'
listTSCANTerminalNodes(x)

Arguments

x

Input SingleCellExperiment object.

analysisName

Algorithm name implemented, should be one of "Pseudotime", "DEG", or "ClusterDEAnalysis".

pathName

Sub folder name within the analysisName. See details.

value

Value to be stored within the pathName or analysisName

Value

Get or set TSCAN results

Details

When analysisName = "Pseudotime", returns the list result from runTSCAN, including the MST structure.

When analysisName = "DEG", returns the list result from runTSCANDEG, including DataFrames containing genes that increase/decrease along each the pseudotime paths. pathName indicates the path index, the available options of which can be listed by listTSCANTerminalNodes.

When analysisName = "ClusterDEAnalysis", returns the list result from runTSCANClusterDEAnalysis. Here pathName needs to match with the useCluster argument when running the algorithm.

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                useReducedDim = "PCA_logcounts")
#> Wed Apr 23 11:37:34 2025 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Wed Apr 23 11:37:34 2025 ...   Identified 2 clusters
#> Wed Apr 23 11:37:34 2025 ... Running TSCAN to estimate pseudotime
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
#> Found more than one class "dist" in cache; using the first, from namespace 'BiocGenerics'
#> Also defined by ‘spam’
#> Wed Apr 23 11:37:35 2025 ...   Clusters involved in path index 2 are: 1, 2
#> Wed Apr 23 11:37:35 2025 ...   Number of estimated paths is 1
results <- getTSCANResults(mouseBrainSubsetSCE, "Pseudotime")