cell.filter: Filter cells

In rezakj/scSeqR: scSeqR; a toolkit to analyze single cell sequencing data types (i.e scRNA-seq) and large numeric matrix files.

Filter cells

Description

This function takes an object of class scSeqR 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 scSeqR.
min.mito	Min ratio of mit genes, defult = 0.
max.mito	Max ratio of mit genes, defult = 1.
min.genes	Min number genes per cell, defult = 0.
max.genes	Max number genes per cell, defult = Inf.
min.umis	Min number UMIs per cell, defult = 0.
max.umis	Max number UMIs per cell, defult = 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, defult = 1.

Value

An object of class scSeqR.

Examples

## Not run: 
cell.filter(my.obj,
   min.mito = 0,
   max.mito = 1,
   min.genes = 0,
   max.genes = Inf,
   min.umis = 0,
   max.umis = Inf)

## End(Not run)

rezakj/scSeqR documentation built on March 28, 2022, 12:17 p.m.