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Calculate the Similarity Matrix

Source: R/getDistMat.R
getDistMat.Rd

Compute the IDER-based similarity matrix for a list of Seurat objects. This function does not regress out batch effects and is designed for use during the initial clustering step.

Usage

getDistMat(
  seu_list,
  verbose = TRUE,
  tmp.initial.clusters = "seurat_clusters",
  method = "trend",
  batch.var = "Batch",
  additional.variate = NULL,
  downsampling.size = 35,
  downsampling.include = TRUE,
  downsampling.replace = TRUE
)

Arguments

seu_list

A list containing Seurat objects. Required.

verbose

Logical. If TRUE, progress messages and a progress bar are displayed. Default is TRUE.

tmp.initial.clusters

Character string specifying one of the column names from Seurat@meta.data that denotes groups, e.g., initial clusters. Default is "seurat_clusters".

method

Character string specifying the method for differential expression analysis. Options are "voom" or "trend" (default is "trend").

batch.var

Character string specifying the metadata column containing batch information. Default is "Batch".

additional.variate

Character vector of additional variates to include in the linear model for regression.

downsampling.size

Numeric value indicating the number of cells to use per group. Default is 35.

downsampling.include

Logical. Whether to include groups with fewer cells than downsampling.size. Default is TRUE.

downsampling.replace

Logical. Whether to sample with replacement for groups smaller than downsampling.size. Default is TRUE.

Value

A list of similarity matrices.

See also

calculateDistMatOneModel