FilterCells: Filter out poor quality cells

In debsin/dropClust: Single Cell Transcriptome Analysis

Description

Keep only those cells (columns) expressing atleast count = min_count in the number of genes specified within the quantile range between ql_th and qh_th.

Usage

FilterCells(object, min_count = 3, ql_th = 0.001, qh_th = 1)

Arguments

object	the SingleCellExperiment object to filter
min_count	integer threshold for expression count
ql_th	quantile at probability with values in [0,1] for lower limit
qh_th	quantile at probability with values in [0,1] for upper limit

Value

SingleCellExperiment object with the bad cells removed

Examples

library(SingleCellExperiment)
counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
object <- SingleCellExperiment(assays = list(counts = counts))
FilterCells(object)

debsin/dropClust documentation built on Nov. 4, 2019, 10:22 a.m.