estimateBackground {transcriptR} | R Documentation

## estimateBackground

### Description

Gene expression is a stochastic process, which often results in substantial expression noise. To obtain a putative set of transcribed regions, it is necessary to identify those regions that are expressed significantly above the background level. Using a Poisson-based approach for estimating the noise distribution from the frequency of the transcribed regions with the low fragments coverage, `estimateBackground` function returns a coverage cutoff value for a specific False Discovery Rate (FDR).

### Usage

    estimateBackground(object, fdr.cutoff = 0.05)

    ## S4 method for signature 'TranscriptionDataSet'
    estimateBackground(object, fdr.cutoff = 0.05)

### Arguments

`object` | A `TranscriptionDataSet` object.
`fdr.cutoff` | `Numeric`. False Discovery Rate cutoff value. Default: 0.05.

### Value

The slots `coverageCutoffFdr` and `coverageCutoff` of the provided `TranscriptionDataSet` object will be updated by the FDR cutoff value used in the calculations and by the corresponding estimated coverage cutoff value, respectively.

### Author(s)

Armen R. Karapetyan

### See Also

`constructTDS` `peakCutoff`

### Examples

    ### Load TranscriptionDataSet object
    data(tds)

    ### Estimate coverage cutoff at different FDR levels
    estimateBackground(object = tds, fdr = 0.01)

[Package transcriptR version 1.8.0 Index]