runTSCANClusterDEAnalysis: Find DE genes between all TSCAN paths rooted from given...

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

Find DE genes between all TSCAN paths rooted from given cluster

Description

This function finds all paths that root from a given cluster useCluster, and performs tests to identify significant features for each path, and are not significant and/or changing in the opposite direction in the other paths. Using a branching cluster (i.e. a node with degree > 2) may highlight features which are responsible for the branching event. MST has to be pre-calculated with runTSCAN.

Usage

runTSCANClusterDEAnalysis(
  inSCE,
  useCluster,
  useAssay = "logcounts",
  fdrThreshold = 0.05
)

Arguments

inSCE	Input SingleCellExperiment object.
useCluster	The cluster to be regarded as the root, has to existing in colData(inSCE)$TSCAN_clusters.
useAssay	Character. The name of the assay to use. This assay should contain log normalized counts. Default "logcounts".
fdrThreshold	Only out put DEGs with FDR value smaller than this value. Default 0.05.

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")
mouseBrainSubsetSCE <- runTSCANClusterDEAnalysis(inSCE = mouseBrainSubsetSCE,
                                         useCluster = 1)

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