pre_pseudotime_matrix: Calculate and return a smoothed pseudotime matrix for the...

In ClusterGVis: One-Step to Cluster and Visualize Gene Expression Data

Calculate and return a smoothed pseudotime matrix for the given gene list

Description

This function takes in a monocle3 object and returns a smoothed pseudotime matrix for the given gene list, either in counts or normalized form. The function first matches the gene list with the rownames of the SummarizedExperiment object, and then orders the pseudotime information. The function then uses smooth.spline to apply smoothing to the data. Finally, the function normalizes the data by subtracting the mean and dividing by the standard deviation for each row.

Usage

pre_pseudotime_matrix(
  cds_obj = NULL,
  assays = c("counts", "normalized"),
  gene_list = NULL
)

Arguments

cds_obj	A monocle3 object
assays	Type of assay to be used for the analysis, either "counts" or "normalized"
gene_list	A vector of gene names

Value

A smoothed pseudotime matrix for the given gene list

ClusterGVis documentation built on April 4, 2025, 2:27 a.m.