filterSCData: Filter Genes and Samples from a Single Cell Object

In mmkhan19/singleCellTK: Interactive Analysis of Single Cell RNA-Seq Data

Filter Genes and Samples from a Single Cell Object

Description

Filter Genes and Samples from a Single Cell Object

Usage

filterSCData(
  inSCE,
  useAssay = "counts",
  deletesamples = NULL,
  removeNoExpress = TRUE,
  removeBottom = 0.5,
  minimumDetectGenes = 1700,
  filterSpike = TRUE
)

Arguments

inSCE	Input SCtkExperiment object. Required
useAssay	Indicate which assay to use for filtering. Default is "counts"
deletesamples	List of samples to delete from the object.
removeNoExpress	Remove genes that have no expression across all samples. The default is true
removeBottom	Fraction of low expression genes to remove from the single cell object. This occurs after removeNoExpress. The default is 0.50.
minimumDetectGenes	Minimum number of genes with at least 1 count to include a sample in the single cell object. The default is 1700.
filterSpike	Apply filtering to Spike in controls (indicated by isSpike). The default is TRUE.

Value

The filtered single cell object.

Examples

data("mouseBrainSubsetSCE")
mouseBrainSubsetSCE <- filterSCData(mouseBrainSubsetSCE,
                                    deletesamples="X1772063061_G11")

mmkhan19/singleCellTK documentation built on March 22, 2022, 7:43 a.m.