estimateBackground {transcriptR} | R Documentation |
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).
estimateBackground(object, fdr.cutoff = 0.05) ## S4 method for signature 'TranscriptionDataSet' estimateBackground(object, fdr.cutoff = 0.05)
object |
A |
fdr.cutoff |
|
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.
Armen R. Karapetyan
### Load TranscriptionDataSet object data(tds) ### Estimate coverage cutoff at different FDR levels estimateBackground(object = tds, fdr = 0.01)