transcriptsToBed {transcriptR} | R Documentation

## transcriptsToBed

### Description

A convenient graphical way to explore the identified transcripts is to visualize them in the UCSC genome browser. The `transcriptsToBed` function returns a file in BED format, which can be directly uploaded to the genome browser. To improve the visual perception, transcripts are color-coded by DNA strand orientation.

### Usage

    transcriptsToBed(object, file, strand.color = c("blue", "red"))

    ## S4 method for signature 'GRanges'
    transcriptsToBed(object, file, strand.color = c("blue",
      "red"))

### Arguments

`object` | A `GRanges` object.
`file` | `Character`. A file name.
`strand.color` | A character vector of length two, specifying color for each DNA strand. Default: c("blue", "red").

### Value

A file in the BED format.

### Author(s)

Armen R. Karapetyan

### See Also

`estimateBackground` UCSC genome browser BED

### Examples

    ### Load TranscriptionDataSet object
    data(tds)

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

    ### Detect transcripts
    detectTranscripts(object = tds, coverage.cutoff = 5, gap.dist = 4000,
    estimate.params = TRUE, combine.by.annot = FALSE, annot = annot)

    ### View detected transcripts
    trx <- getTranscripts(tds)

    ### Export to BED
    # transcriptsToBed(object = trx, file = "transcripts.bed",
    # strand.color = c("blue", "red"))

[Package transcriptR version 1.8.0 Index]