Perform cell and gene QC on a Seurat object

This is a convenience wrapper of PerformSeuratCellQC() and PerformGeneQC() for a single sample, as done by LoadSeuratAndPerformQC() per sample before the samples are merged.

Usage

PerformSeuratQC(object, cell_qc = NULL, gene_qc = NULL)

Arguments

object

Seurat object of a single sample

cell_qc

Cell QC criteria. It is an expression string to pass to dplyr::filter function to filter the cells. It can also be a list of expressions, where the names of the list are sample names. You can have a default expression in the list with the name "DEFAULT" for the samples that are not listed.

gene_qc

Gene QC criteria A list containing the following fields:

• min_cells: Minimum number of cells a gene should be expressed in to be kept

• excludes: A string or strings to exclude certain genes. Regular expressions are supported. Multiple strings can also be separated by commas in a single string.

Value

The Seurat object with the .QC column in meta.data and, if gene_qc is given, the gene QC results in @misc$gene_qc

Examples

# \donttest{
obj <- PerformSeuratQC(
    SeuratObject::pbmc_small,
    cell_qc = "nFeature_RNA > 40",
    gene_qc = list(min_cells = 3)
)
table(obj$.QC)
#> 
#> FALSE  TRUE 
#>    15    65 
head(obj@misc$gene_qc)
#>                 Sample  Feature Count   QC
#> MS4A1    SeuratProject    MS4A1    12 TRUE
#> CD79B    SeuratProject    CD79B    23 TRUE
#> CD79A    SeuratProject    CD79A    13 TRUE
#> HLA-DRA  SeuratProject  HLA-DRA    55 TRUE
#> TCL1A    SeuratProject    TCL1A     8 TRUE
#> HLA-DQB1 SeuratProject HLA-DQB1    30 TRUE
# }