qc.stats {iCellR}

Calculate the number of UMIs and genes per cell and percentage of mitochondrial genes per cell and cell cycle genes.

Description

This function takes data frame and calculates the number of UMIs, genes per cell and percentage of mitochondrial genes per cell and cell cycle genes.

Usage

qc.stats(
  x = NULL,
  which.data = "raw.data",
  mito.genes = NULL,
  s.phase.genes = s.phase,
  g2m.phase.genes = g2m.phase
)

Arguments

x

A data frame containing gene counts for cells.

which.data

Choose from "raw.data" or "main.data", "imputed.data", default = "raw.data".

mito.genes

A character vector of mitochondrial genes names , default is the genes starting with mt.

s.phase.genes

A character vector of gene names for S phase, default = s.phase.

g2m.phase.genes

A character vector of gene names for G2 and M phase, default = g2m.phase.

Value

The data frame object