transcriptsToBed {transcriptR} | R Documentation |
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.
transcriptsToBed(object, file, strand.color = c("blue", "red")) ## S4 method for signature 'GRanges' transcriptsToBed(object, file, strand.color = c("blue", "red"))
object |
A |
file |
|
strand.color |
A character vector of length two, specifying color for each DNA strand. Default: c("blue", "red"). |
A file in the BED format.
Armen R. Karapetyan
estimateBackground
UCSC genome browser
BED
### 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"))