pre_pseudotime_matrix

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.

Streamlining the clustering and visualization of time-series gene expression data from RNA-Seq experiments, this tool supports fuzzy c-means and k-means clustering algorithms. It is compatible with outputs from widely-used packages such as 'Seurat', 'Monocle', and 'WGCNA', enabling seamless downstream visualization and analysis. See Lokesh Kumar and Matthias E Futschik (2007) <doi:10.6026/97320630002005> for more details.

Junjun Lao

ClusterGVis

One-Step to Cluster and Visualize Gene Expression Data

Jun Zhang

pre_pseudotime_matrix function

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

Arguments

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

<dl>

<dt>cds_obj</dt>
<dd>A monocle3 object</dd>


<dt>assays</dt>
<dd>Type of assay to be used for the analysis, either "counts" or "normalized"</dd>


<dt>gene_list</dt>
<dd>A vector of gene names</dd>

</dl>

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

Description

Usage

Value

Arguments