iCellR (version 1.6.1)

cell.filter: Filter cells

Description

This function takes an object of class iCellR and filters the raw data based on the number of UMIs, genes per cell, percentage of mitochondrial genes per cell, genes, gene expression and cell ids.

Usage

cell.filter(
  x = NULL,
  min.mito = 0,
  max.mito = 1,
  min.genes = 0,
  max.genes = Inf,
  min.umis = 0,
  max.umis = Inf,
  filter.by.cell.id = "character",
  keep.cell.id = "character",
  filter.by.gene = "character",
  filter.by.gene.exp.min = 1
)

Arguments

x

An object of class iCellR.

min.mito

Min rate for mitochondrial gene expression per cell, default = 0.

max.mito

Max rate for mitochondrial gene expression per cell, default = 1.

min.genes

Min number genes per cell, default = 0.

max.genes

Max number genes per cell, default = Inf.

min.umis

Min number UMIs per cell, default = 0.

max.umis

Max number UMIs per cell, default = Inf.

filter.by.cell.id

A character vector of cell ids to be filtered out.

keep.cell.id

A character vector of cell ids to keep.

filter.by.gene

A character vector of gene names to be filtered by thier expression. If more then one gene is defined it would be OR not AND.

filter.by.gene.exp.min

Minimum gene expression to be filtered by the genes set in filter.by.gene, default = 1.

Value

An object of class iCellR.

Examples

# NOT RUN {
demo.obj <- cell.filter(demo.obj,
                       min.mito = 0,
                       max.mito = 0.05 ,
                       min.genes = 100,
                       max.genes = 2500,
                       min.umis = 0,
                       max.umis = Inf)

message([e-mail])

# }