distmat: Calculate scSLAM-seq based distance matrices

In HetSeq: Identifying Modulators of Cellular Responses Leveraging Intercellular Heterogeneity

Calculate scSLAM-seq based distance matrices

Description

This function calculates distances matrices between cells of different time points based on metabolic labeling RNA profiles.

Usage

distmat(prev.t, next.t, prevAssay, nextAssay, gene_subset = NULL)

Arguments

prev.t	Cells to be used from the previous time point in distance matrix calculation.
next.t	Cells to be used from the next time point in distance matrix calculation.
prevAssay	Name of the expression assay of cells from the previous time point.
nextAssay	Name of the expression assay of cells from the next time point.
gene_subset	Set a subset of genes on which trajectories should be calculated. Other genes will be disregarded.

Value

Distance matrix between cells from two time points.

Examples

# Full vignette available on https://grandr.erhard-lab.de/articles/web/hetseq.html

  obj.list <- SplitObject(seuratObject, split.by = "time")
  D.list=list(
   distmat(treatment.list[["0h"]],treatment.list[["2h"]], "RNA", "prevRNA"),
   distmat(treatment.list[["2h"]],treatment.list[["4h"]], "RNA", "prevRNA")
  )

HetSeq documentation built on April 4, 2025, 2:03 a.m.