filter_data: Filter cells based on the number of genes and mitochondrial...

In igordot/scooter: Streamlined scRNA-Seq Analysis Pipeline

Filter cells based on the number of genes and mitochondrial reads.

Description

Filter out cells based on minimum and maximum number of genes and maximum percentage mitochondrial reads. If cutoffs are not provided, the min_genes will be the 0.02 quantile, and the max genes will be 0.98 quantile and the mitochondrial percentage will be 10

Usage

filter_data(
  data,
  log_file = NULL,
  min_genes = NULL,
  max_genes = NULL,
  max_mt = 10
)

Arguments

data	A tibble with metadata.
log_file	Log file.
min_genes	Minimum number of genes per cell.
max_genes	Maximim number of genes per cell.
max_mt	Maximum percentage of mitochondrial reads per cell.

Value

Filtered data

igordot/scooter documentation built on Nov. 20, 2023, 5:55 a.m.