basicSeuratProc: Create and preprocess a Seurat object

Description Usage Arguments Value Examples

Description

Create and preprocess a Seurat object

Usage

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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

Examples

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library(Seurat)
panel.preprocessed <- lapply(conosPanel::panel, basicSeuratProc)

conos documentation built on Feb. 23, 2021, 9:06 a.m.