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CIDER (version 0.99.1)

getDistMat: Calculate the Similarity Matrix

Description

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

Usage

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

Value

A list of similarity matrices

Arguments

seu_list

A list containing Seurat objects. Required.

verbose

Print the message and progress bar (default: TRUE)

tmp.initial.clusters

One of the colnames from `Seurat@meta.data`. Used as the group. Default: "seurat_clusters"

method

Methods for DE analysis. Options: "voom" or "trend" (default)

additional.variate

additional variate to include into the linear model to regress out

downsampling.size

Number of cells used per group. Default: 35

downsampling.include

Whether to include the group of size smaller than `downsampling.size`. Default: TRUE

downsampling.replace

Whether to use `replace` in sampling for group of size smaller than `downsampling.size` if they are kept. Default: TRUE

Author

Zhiyuan Hu

See Also

calculateDistMatOneModel