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

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

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

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

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

listTSCANResults(x)

# S4 method for SingleCellExperiment
listTSCANResults(x)

listTSCANTerminalNodes(x)

# S4 method for 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 Jan 10 17:42:26 2024 ... Running 'scran SNN clustering' with 'louvain' algorithm
#> Wed Jan 10 17:42:27 2024 ...   Identified 2 clusters
#> Wed Jan 10 17:42:27 2024 ... Running TSCAN to estimate pseudotime
#> Wed Jan 10 17:42:28 2024 ...   Clusters involved in path index 2 are: 1, 2
#> Wed Jan 10 17:42:28 2024 ...   Number of estimated paths is 1
results <- getTSCANResults(mouseBrainSubsetSCE, "Pseudotime")