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.
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
)A list of similarity matrices.
A list containing Seurat objects. Required.
Logical. If TRUE, progress messages and a progress bar are displayed. Default is TRUE.
Character string specifying one of the column names from Seurat@meta.data
that denotes groups, e.g., initial clusters.
Default is "seurat_clusters".
Character string specifying the method for differential expression analysis. Options are "voom" or "trend" (default is "trend").
Character string specifying the metadata column containing batch information. Default is "Batch".
Character vector of additional variates to include in the linear model for regression.
Numeric value indicating the number of cells to use per group. Default is 35.
Logical. Whether to include groups with fewer cells than
downsampling.size. Default is TRUE.
Logical. Whether to sample with replacement for groups
smaller than downsampling.size. Default is TRUE.
calculateDistMatOneModel