filterSCData {singleCellTK} | R Documentation |
Filter Genes and Samples from a Single Cell Object
filterSCData(inSCE, useAssay = "counts", deletesamples = NULL, removeNoExpress = TRUE, removeBottom = 0.5, minimumDetectGenes = 1700, filterSpike = TRUE)
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. |
The filtered single cell object.
data("mouseBrainSubsetSCE") mouseBrainSubsetSCE <- filterSCData(mouseBrainSubsetSCE, deletesamples="X1772063061_G11")