count_filter {ERSSA} | R Documentation

## Filter RNA-seq expression table

### Description

`count_filter` function filters the RNA-seq count table to remove non- and low-expression genes at an defined average CPM cutoff (Default=1).

### Usage

    count_filter(count_table = NULL, cutoff = 1)

### Arguments

`count_table` | A RNA-seq count matrix with genes on each row and samples on each column.
`cutoff` | Any gene with average CPM below this cutoff value will be filtered out.

### Value

The filtered count table.

### Author(s)

Zixuan Shao, Zixuanshao.zach@gmail.com

### Examples

    # load simple GTeX example count table
    # example dataset containing 1000 genes, 4 replicates
    data(count_table.partial, package = "ERSSA")

    #filter the counts
    count_table.filtered.partial = count_filter(count_table.partial)

[Package ERSSA version 1.6.0 Index]