Apply QC filters to Seurat Object

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

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

Nicholas Mikolajewicz