SingleR.CreateSeurat: Wrapper function to create a Seurat object

In dviraran/SingleR: Reference-based single-cell RNA-seq annotation

Description

Wrapper function to create a Seurat object

Usage

SingleR.CreateSeurat(project.name, sc.data, min.genes = 200,
  min.cells = 2, regress.out = "nUMI", npca = 10, resolution = 0.8,
  temp.dir = NULL)

Arguments

project.name	the project name
sc.data	a matrix of single cell expression data
min.genes	Include cells where at least this many genes are detected.
min.cells	include genes with detected expression in at least this many cells. Will subset the raw.data matrix as well. To reintroduce excluded genes, create a new object with a lower cutoff.
regress.out	variables to regress out (previously latent.vars in RegressOut). For example, nUMI, or percent.mito.
npca	a vector of the dimensions to use in construction of the clustering and tSNE plot
resolution	clustering resolution. See Seurat manual for more details.
temp.dir	used by FindClusters function.

Value

a Seurat object

dviraran/SingleR documentation built on April 21, 2020, 3:23 p.m.