getTSCANResults: getTSCANResults accessor function

In compbiomed/singleCellTK: Comprehensive and Interactive Analysis of Single Cell RNA-Seq Data

getTSCANResults accessor function

Description

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

Usage

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

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

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

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

listTSCANResults(x)

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

listTSCANTerminalNodes(x)

## S4 method for signature '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

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.

Value

Get or set TSCAN results

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                useReducedDim = "PCA_logcounts")
results <- getTSCANResults(mouseBrainSubsetSCE, "Pseudotime")

compbiomed/singleCellTK documentation built on Feb. 10, 2024, 3:32 a.m.