basicSeuratProc: Create and preprocess a Seurat object

In kharchenkolab/conos: Clustering on Network of Samples

Create and preprocess a Seurat object

Description

Create and preprocess a Seurat object

Usage

basicSeuratProc(
  count.matrix,
  vars.to.regress = NULL,
  verbose = TRUE,
  do.par = TRUE,
  n.pcs = 100,
  cluster = TRUE,
  tsne = TRUE,
  umap = FALSE
)

Arguments

count.matrix	gene count matrix
vars.to.regress	variables to regress with Seurat (default=NULL)
verbose	boolean Verbose mode (default=TRUE)
do.par	boolean Use parallel processing for regressing out variables faster (default=TRUE)
n.pcs	numeric Number of principal components (default=100)
cluster	boolean Whether to perform clustering (default=TRUE)
tsne	boolean Whether to construct tSNE embedding (default=TRUE)
umap	boolean Whether to construct UMAP embedding, works only for Seurat v2.3.1 or higher (default=FALSE)

Value

Seurat object

kharchenkolab/conos documentation built on Feb. 28, 2024, 6:03 a.m.