filterSCData {singleCellTK} | R Documentation

## 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")

[Package singleCellTK version 1.2.3 Index]