cell_clusters_identify: Cluster cells from a selected gene module list.

In juliendelile/Antler: ANother Transcriptome Lineage ExploreR

Description

A text file containing the gene modules is written to the Antler output folder.

Arguments

name	character string. The name of the cell clusters object. Multiple cell clusters objects under different names can be stored.
gene_modules_name	character string. The name of the list of gene modules from which the cell-to-cell distance will be calculated.
method	character string. The clustering method to use. Currently only hclust is available (using "ward.D2" as agglomeration method).
cell_cell_dist	numeric matrix. Optionally a matrix containing the cell-to-cell distances can be provided. If NA (default), the matrix is calculated internally using Euclidean distance.
logscaled	logical. If TRUE (default), the gene expression level are log-transformed and z-normalized before calculating the cell-to-cell distance. If FALSE, no transformation is applied to the levels.
num_clusters	an integer value indicating the number of cell clusters. If NULL (default) a heuristic method is used to find the optimal number of clusters.
data_status	character string. Specifies whether the gene expression levels to be used are raw ("Raw"), normalized ("Normalized") or have been imputed ("Smoothed"). Default to "Normalized".
process_plots	a logical value indicating whether to render the heuristic trade-off determining the number clusters. Default to FALSE.

juliendelile/Antler documentation built on June 19, 2021, 9 a.m.