Create and preprocess a Seurat object
Create and preprocess a Seurat object
basicSeuratProc( count.matrix, vars.to.regress = NULL, verbose = TRUE, do.par = TRUE, n.pcs = 100, cluster = TRUE, tsne = TRUE, umap = FALSE )
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) |
Seurat object
library(Seurat) panel.preprocessed <- lapply(conosPanel::panel, basicSeuratProc)
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