plotErrorRate {transcriptR} | R Documentation

## plotErrorRate

### Description

A simple helper function that plot results of `estimateGapDistance` function call.

### Usage

    plotErrorRate(object, color = c("#1B9E77", "#D95F02", "#7570B3"),
      xlab = "Gap distance (kb)", ylab = "Error rate", ...)

    ## S4 method for signature 'TranscriptionDataSet'
    plotErrorRate(object, color = c("#1B9E77",
      "#D95F02", "#7570B3"), xlab = "Gap distance (kb)", ylab = "Error rate",
      ...)

### Arguments

`object` | A `TranscriptionDataSet` object.
`color` | `Character`. Colors to be used to plot estimated errors.
`xlab` | `Character`. Label of the x-axis.
`ylab` | `Character`. Lable of the y-axis.
`...` | Further arguments passed to plot.

### Details

The tested gap distances are plotted on the x-axis and corresponding error rates on the y-axis. Three curved lines depict the two error types calculated by `estimateGapDistance` and the sum of both errors. The vertical dashed line depicts the gap distance with the smallest sum of two errors.

### Value

plot

### Author(s)

Armen R. Karapetyan

### See Also

`estimateGapDistance`

### 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)

    plotErrorRate(object = tds, lwd = 2)

[Package transcriptR version 1.10.1 Index]