runTSCANDEG: Test gene expression changes along a TSCAN trajectory path

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

Test gene expression changes along a TSCAN trajectory path

Description

Wrapper for identifying genes with significant changes with respect to one of the TSCAN pseudotime paths

Usage

runTSCANDEG(inSCE, pathIndex, useAssay = "logcounts", discardCluster = NULL)

Arguments

inSCE	Input SingleCellExperiment object.
pathIndex	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.
useAssay	Character. The name of the assay to use for testing the expression change. Should be log-normalized. Default "logcounts"
discardCluster	Cluster(s) which are not of use or masks other interesting effects can be discarded. Default NULL.

Value

The input inSCE with results updated in metadata.

Author(s)

Nida Pervaiz

Examples

data("mouseBrainSubsetSCE", package = "singleCellTK")
mouseBrainSubsetSCE <- runTSCAN(inSCE = mouseBrainSubsetSCE,
                                useReducedDim = "PCA_logcounts")
terminalNodes <- listTSCANTerminalNodes(mouseBrainSubsetSCE)
mouseBrainSubsetSCE <- runTSCANDEG(inSCE = mouseBrainSubsetSCE,
                                   pathIndex = terminalNodes[1])

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