runTSCAN: Run TSCAN to obtain pseudotime values for cells

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

Run TSCAN to obtain pseudotime values for cells

Description

Wrapper for obtaining a pseudotime ordering of the cells by projecting them onto the minimum spanning tree (MST)

Usage

runTSCAN(
  inSCE,
  useReducedDim = "PCA",
  cluster = NULL,
  starter = NULL,
  seed = 12345
)

Arguments

inSCE	Input SingleCellExperiment object.
useReducedDim	Character. A low-dimension representation in reducedDims, will be used for both clustering if cluster not specified and MST construction. Default "PCA".
cluster	Grouping for each cell in inSCE. A vector with equal length to the number of the cells in inSCE, or a single character for retriving colData variable. Default NULL, will run runScranSNN to obtain.
starter	Character. Specifies the starting node from which to compute the pseudotime. Default NULL, will select an arbitrary node.
seed	An integer. Random seed for clustering if cluster is not specified. Default 12345.

Value

The input inSCE object with pseudotime ordering of the cells along the paths and the cluster label stored in colData, and other unstructured information in metadata.

Author(s)

Nida Pervaiz

Examples

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

compbiomed/singleCellTK documentation built on Oct. 27, 2024, 3:26 a.m.