Filter Genes and Samples from a Single Cell Object

Source: R/miscFunctions.R

Filter Genes and Samples from a Single Cell Object

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

Arguments

inSCE

Input SingleCellExperiment 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

if (FALSE) {
data("mouseBrainSubsetSCE")
mouseBrainSubsetSCE <- filterSCData(mouseBrainSubsetSCE,
                                    deletesamples="X1772063061_G11")
}