getDistMat {CIDER}R Documentation

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
)

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

Value

A list of similarity matrices

Author(s)

Zhiyuan Hu

See Also

calculateDistMatOneModel


[Package CIDER version 0.99.0 Index]