Read10xData: Create Seurat Object from sparse data matrices provided by...

Description Usage Arguments Value

View source: R/Read10xData.R

Description

This function create a Seurat object from a 10x output directory by loading a matrix (matrix.mtx.gz), a barcode file (barcodes.tsv.gz) and a feature file (features.tsv.gz) from the current directory.

Usage

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Read10xData(
  data.dir,
  output.dir = NULL,
  min.cells = 3,
  min.features = 200,
  mt.pattern = "^mt-",
  project.name = "SeuratProject",
  ...
)

Arguments

data.dir

Directory containing the matrix.mtx, genes.tsv (or features.tsv), and barcodes.tsv files provided by 10X. A vector or named vector can be given in order to load several data directories. If a named vector is given, the cell barcode names will be prefixed with the name.

output.dir

Path to the destination folder of saved files

min.cells

Include features detected in at least this many cells. Will subset the counts matrix as well. To reintroduce excluded features, create a new object with a lower cutoff.

min.features

Include cells where at least this many features are detected.

mt.pattern

Regex pattern of the mitochondrial genes ('^MT-' or '^mt-')

project.name

Name of the project/object used for titles in plots

...

Arguments passed to as.sparse

Value

A Seurat Object and its QC plots


Theob0t/scEasyPip documentation built on Dec. 18, 2021, 4:10 p.m.