filter_cells {ccfindR} | R Documentation

## Filter cells with quality control criteria

### Description

Remove low quality cell entries from object

### Usage

    filter_cells(object, umi.min = 0, umi.max = Inf, plot = TRUE,
      remove.zeros = TRUE)

### Arguments

`object` | `scNMFSet` object
`umi.min` | Minimum UMI count for cell filtering
`umi.max` | Maximum UMI count for cell filtering
`plot` | If `TRUE`, the UMI count distribution of all cells will be displayed. Cells selected are colored red.
`remove.zeros` | Remove rows/columns containing zeros only

### Details

Takes as input `scNMFSet` object and plots histogram of UMI counts for each cell. Optionally, cells are filtered using minimum and maximum UMI counts. The resulting object is returned after removing empty rows and columns, if any.

### Value

`scNMFSet` object with cells filtered.

### Examples

    set.seed(1)
    s <- scNMFSet(matrix(stats::rpois(n=1200,lambda=3),40,30))
    s <- filter_cells(s,umi.min=10^2.0,umi.max=10^2.1)

[Package ccfindR version 1.4.2 Index]