estimateGapDistance-methods: estimateGapDistance

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

Description

The ultimate goal of transcriptR is to identify continuous regions of transcription. However, in some areas of the genome it is not possible to detect transcription, because of the presence of the low mappability regions and (high copy number) repeats. Sequencing reads can not be uniquely mapped to these positions, leading to the formation of gaps in otherwise continuous coverage profiles and segmentation of transcribed regions into multiple smaller fragments. The gap distance describes the maximum allowed distance between adjacent fragments to be merged into one transcript. To choose the optimal value for the gap distance, the detected transcripts should largely be in agreement with available reference annotations. To accomplish this, the function is build on the methodology proposed by Hah et al. (Cell, 2011). In brief, the two types of erros are defined:

• dissected error - the ratio of annotations that is segmented into two or more fragments.

• merged error - the ratio of non-overlapping annotations that merged by mistake in the experimental data.

There is an interdependence between two types of errors. Increasing the gap distance decreases the dissected error, by detecting fewer, but longer transcripts, while the merged error will increase as more detected transcripts will span multiple annotations. The gap distance with the lowest sum of two error types is chosen as the optimal value.

Usage

estimateGapDistance(object, annot, coverage.cutoff, filter.annot = TRUE,
  fpkm.quantile = 0.25, gap.dist.range = seq(from = 0, to = 10000, by =
  100))

## S4 method for signature 'TranscriptionDataSet,GRanges'
estimateGapDistance(object, annot,
  coverage.cutoff, filter.annot = TRUE, fpkm.quantile = 0.25,
  gap.dist.range = seq(from = 0, to = 10000, by = 100))

Arguments

object	A TranscriptionDataSet object.
annot	GRanges. Reference annotations.
coverage.cutoff	Numeric. A cutoff value to discard regions with the low fragments coverage, representing expression noise. By default, the value stored in the coverageCutoff slot of the supplied TranscriptionDataSet object is used. The optimal cutoff value can be calculated by estimateBackground function call.
filter.annot	Logical. Whether to filter out lowly expressed annotations, before estimating error rates. Default: TRUE.
fpkm.quantile	Numeric. A number in a range (0, 1). A cutoff value used for filtering lowly expressed annotations. The value corresponds to the FPKM quantile estimated for the supplied annotations. Default: 0.25.
gap.dist.range	A numeric vector specifying a range of gap distances to test. By default, the range is from 0 to 10000 with a step of 100.

Value

The slot gapDistanceTest of the provided TranscriptionDataSet object will be updated by the data.frame, containing estimated error rates for each tested gap distance (see getTestedGapDistances, for the details).

Author(s)

Armen R. Karapetyan

References

Hah N, Danko CG, Core L, Waterfall JJ, Siepel A, Lis JT, Kraus WL. A rapid, extensive, and transient transcriptional response to estrogen signaling in breast cancer cells. Cell. 2011.

See Also

constructTDS plotErrorRate getTestedGapDistances

Examples

### Load TranscriptionDataSet object
data(tds)

### Load reference annotations (knownGene from UCSC)
data(annot)

### Estimate gap distance minimazing error rate
### Define the range of gap distances to test
gdr <- seq(from = 0, to = 10000, by = 1000)

estimateGapDistance(object = tds, annot = annot, coverage.cutoff = 5,
filter.annot = FALSE, gap.dist.range = gdr)

### View estimated gap distance
tds

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