CreateSeuratObj: Wrapper around Seurat::CreateSeuratObject

In bimberlabinternal/CellMembrane: A package with high-level wrappers and pipelines for single-cell RNA-seq tools

Wrapper around Seurat::CreateSeuratObject

Description

Create Seurat object from count data (usually from Read10X()). This also sets pct.mito.

Usage

CreateSeuratObj(
  seuratData,
  datasetId,
  datasetName = NULL,
  minFeatures = 25,
  minCells = 0,
  mitoGenesPattern = "^MT-",
  annotateMitoFromReferenceIfNoHitsFound = TRUE
)

Arguments

seuratData	Seurat input data, usually from Read10X().
datasetId	This will be used as a prefix for barcodes, and stored in metadata. Also used as the project name for the Seurat object.
datasetName	An optional print-friendly name that will be stored in metadata
minFeatures	Include cells where at least this many features are detected.
minCells	Include features detected in at least this many cells.
mitoGenesPattern	The expression to use when identifying mitochondrial genes
annotateMitoFromReferenceIfNoHitsFound	If true, a list of mitochondrial genes, taken from (https://en.wikipedia.org/wiki/Category:Human_mitochondrial_genes) will be used to calculate p.mito

Value

A Seurat object with p.mito calculated.

bimberlabinternal/CellMembrane documentation built on Oct. 16, 2024, 6:53 a.m.