Filter Genes and Samples from a Single Cell Object
filterSCData( inSCE, useAssay = "counts", deletesamples = NULL, removeNoExpress = TRUE, removeBottom = 0.5, minimumDetectGenes = 1700, filterSpike = TRUE )
Input SCtkExperiment object. Required
Indicate which assay to use for filtering. Default is "counts"
List of samples to delete from the object.
Remove genes that have no expression across all samples. The default is true
Fraction of low expression genes to remove from the single cell object. This occurs after removeNoExpress. The default is 0.50.
Minimum number of genes with at least 1 count to include a sample in the single cell object. The default is 1700.
Apply filtering to Spike in controls (indicated by isSpike). The default is TRUE.
The filtered single cell object.
data("mouseBrainSubsetSCE") mouseBrainSubsetSCE <- filterSCData(mouseBrainSubsetSCE, deletesamples="X1772063061_G11")