filter_scExp {ChromSCape} | R Documentation

## Filter cells and features

### Description

Function to filter out cells & features from SingleCellExperiment based on total count per cell, number of cells 'ON' in features and top covered cells that might be doublets.

### Usage

    filter_scExp(
      scExp,
      min_cov_cell = 1600,
      quant_removal = 95,
      min_count_per_feature = 10,
      verbose = TRUE
    )

### Arguments

`scExp` | A SingleCellExperiment object.
`min_cov_cell` | Minimum counts for each cell. (1600)
`quant_removal` | Centile of cell counts above which cells are removed. (95)
`min_count_per_feature` | Minimum number of reads per feature (10).
`verbose` | (TRUE)

### Value

Returns a filtered SingleCellExperiment object.

### Examples

    scExp = create_scExp(create_scDataset_raw()$mat,create_scDataset_raw()$annot)
    scExp. = filter_scExp(scExp)

    # No feature filtering (all features are valuable)
    scExp. = filter_scExp(scExp,min_count_per_feature=30)

    # No cell filtering (all features are valuable)
    scExp. = filter_scExp(scExp,min_cov_cell=0,quant_removal=100)

[Package ChromSCape version 1.2.62 Index]