clean.counts {scde} | R Documentation

## Filter counts matrix

### Description

Filter counts matrix based on gene and cell requirements

### Usage

    clean.counts(counts, min.lib.size = 1800, min.reads = 10,
      min.detected = 5)

### Arguments

`counts` | read count matrix. The rows correspond to genes, columns correspond to individual cells
`min.lib.size` | Minimum number of genes detected in a cell. Cells with fewer genes will be removed (default: 1.8e3)
`min.reads` | Minimum number of reads per gene. Genes with fewer reads will be removed (default: 10)
`min.detected` | Minimum number of cells a gene must be seen in. Genes not seen in a sufficient number of cells will be removed (default: 5)

### Value

a filtered read count matrix

### Examples

    data(pollen)
    dim(pollen)
    cd <- clean.counts(pollen)
    dim(cd)

[Package scde version 2.14.0 Index]