RunQC: Perform QC on single cell RNA-seq data with seurat, store all...

In Morriseylab/scExtras: Single cell data analysis helper functions

Perform QC on single cell RNA-seq data with seurat, store all stats and return seurat object

Description

Perform QC on single cell RNA-seq data with seurat, store all stats and return seurat object

Usage

RunQC(
  object,
  org = "mouse",
  filter = T,
  LowerFeatureCutoff = 200,
  UpperFeatureCutoff = "MAD",
  UpperMitoCutoff = 5,
  doubletdetection = T,
  dir
)

Arguments

object	Seurat object
org	Organism (mouse/human)
filter	Specify whether to filter data
LowerFeatureCutoff	Lower value for Feature cutoff
UpperMitoCutoff	Upper Mito Pecent cuoff default is 0.05
doubletdetection	Logical to specify if you want to run scds doublet detection
dir	Output directory for QC files
UpperfeatureCutoff	Upper bound, can be an integer or if set to MAD will be 3 median + 3*MAD

Value

Seurat object

Examples

scrna = RunQC(object=scrna,org="mouse",filter = T,LowerFeatureCutoff=200,UpperFeatureCutoff="MAD",UpperMitoCutoff=0.05,doubletdetection = T)

Morriseylab/scExtras documentation built on July 10, 2024, 6:41 a.m.