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