bb_qc: A function to run qc tests on cds objects.

In blaserlab/blaseRtools: R Tools for Blaser Lab Data Analysis

A function to run qc tests on cds objects.

Description

A function to run qc tests on cds objects.

Usage

bb_qc(
  cds,
  cds_name,
  genome = c("human", "mouse", "zfish"),
  nmad_mito = 2,
  nmad_detected = 2,
  max_mito = NULL,
  min_log_detected = NULL
)

Arguments

cds	A cell data set object to run qc functions on
cds_name	The name of the cds
genome	The species to use for identifying mitochondrial genes. Choose from "human", "mouse", "zfish", "human_mouse" for pdx.
max_mito	Manual cutoff for mitochondrial percentage. May be more strict, i.e. lower, than the automated cutoff but not less strict, Default: NULL
min_log_detected	Manual cutoff for log detected features. May be more strict, i.e. higher, than the automated cutoff not not less strict, Default: NULL

Value

A list of qc objects

blaserlab/blaseRtools documentation built on April 14, 2025, 6:04 p.m.