estimateBackground-methods: estimateBackground

In transcriptR: An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

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)

transcriptR documentation built on Nov. 8, 2020, 8:12 p.m.