filterSeurat: Apply QC filters to Seurat Object

In NMikolajewicz/scMiko: scRNAseq analysis functions. Developed using Seurat framework.

Apply QC filters to Seurat Object

Description

Filter scRNAseq data by gene/cell, unmatch rate and mitochondrial content.

Usage

filterSeurat(
  so,
  RNA.upperlimit = 9000,
  RNA.lowerlimit = 200,
  mt.upperlimit = 60,
  unmatch.low = 0,
  unmatch.high = 1,
  set_names = NULL
)

Arguments

so	Seurat Object
RNA.upperlimit	Upper limit threshold for genes/cell
RNA.lowerlimit	Lower limit threshold for genes/cell
mt.upperlimit	Numeric [0, 100]. Upper limit threshold for microchondiral content.
unmatch.low	Numeric [0,1]. Lower limit threshold for unmatch rate. Default is 0. Ignored if data is not from sciRNA-seq3 pipeline.
unmatch.high	Numeric [0,1]. Upper limit threshold for unmatch rate. Default is 1. Ignored if data is not from sciRNA-seq3 pipeline.
set_names	Character specifying dataset name. Optional.

Value

List containing seurat object, filter summary statistics, and filter breakdown list

Author(s)

Nicholas Mikolajewicz

NMikolajewicz/scMiko documentation built on June 28, 2023, 1:41 p.m.