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Seurat basic QC

Source: R/basic.R
seurat_basic_qc.Rd

Calculates mitochondrial and hemoglobin percentages, filters cells by QC thresholds, and optionally plots QC metrics before and after filtering.

Usage

seurat_basic_qc(
  seurat_obj,
  nFeature_RNA_low = 200,
  nFeature_RNA_high = 7500,
  nCount_RNA_high = 10000,
  percent_mt_high = 10,
  percent_HB_high = 1,
  out_path = NULL,
  save_plot = FALSE,
  verbose = TRUE
)

Arguments

seurat_obj

A Seurat object.

nFeature_RNA_low

Lower boundary for number of features per cell. Default: 200.

nFeature_RNA_high

Upper boundary for number of features per cell. Default: 7500.

nCount_RNA_high

Upper boundary for number of counts per cell. Default: 10000.

percent_mt_high

Upper boundary for mitochondrial percentage. Default: 10.

percent_HB_high

Upper boundary for hemoglobin percentage. Default: 1.

out_path

Character. Directory to save QC plots. Required if save_plot is T.

save_plot

Logical. Whether to save QC plots. Default: FALSE.

verbose

Logical. Whether to print leo.log messages. Default: TRUE.

Value

A filtered Seurat object.