filterLowCountGenes {TCC} | R Documentation

## Filter genes from a TCC-class object

### Description

This function takes a TCC object and returns a new TCC object without genes having low count tags across samples. The threshold is configurable with `low.count` parameter.

### Usage

    filterLowCountGenes(tcc, low.count = 0)

### Arguments

`tcc` | TCC-class object.
`low.count` | numeric value (>= 0) specifying the threshold for filtering genes. The higher value indicates the more numbers of genes to be filtered out.

### Value

TCC-class object consisting of genes whose total counts across samples is higher than the `low.count` value.

### Examples

    # Filtering genes with zero counts across samples (default) from
    # a hypothetical count dataset that originally has 1,000 genes.
    data(hypoData)
    group <- c(1, 1, 1, 2, 2, 2)
    tcc <- new("TCC", hypoData, group)
    dim(tcc$count)
    tcc <- filterLowCountGenes(tcc)
    dim(tcc$count)

    # Filtering genes with 10 counts across samples from hypoData.
    data(hypoData)
    group <- c(1, 1, 1, 2, 2, 2)
    tcc <- new("TCC", hypoData, group)
    dim(tcc$count)
    tcc <- filterLowCountGenes(tcc, 10)
    dim(tcc$count)

[Package TCC version 1.28.0 Index]