peaksToBed {transcriptR} | R Documentation |
A convenient way to explore output of the predictions made on the ChIP peaks is to visualize them in the UCSC genome browser. The peaksToBed function returns a file in BED format, which can be uploaded directly to the genome browser. To improve the visual perception, peaks are color-coded by the predicted strand.
peaksToBed(object, file, strand.pred.color = c("blue", "red", "green4", "black"), gene.associated.peaks = TRUE) ## S4 method for signature 'ChipDataSet' peaksToBed(object, file, strand.pred.color = c("blue", "red", "green4", "black"), gene.associated.peaks = TRUE)
object |
A |
file |
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strand.pred.color |
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gene.associated.peaks |
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A file in the BED format.
Armen R. Karapetyan
constructCDS
predictTssOverlap
predictStrand
UCSC genome browser
BED
### Load ChipDataSet object data(cds) ### Load TranscriptionDataSet object data(tds) ### Classify peaks on gene associated and background predictTssOverlap(object = cds, feature = "pileup", p = 0.75) ### Predict peak 'strandedness' predictStrand(cdsObj = cds, tdsObj = tds, coverage.cutoff = 5, quant.cutoff = 0.1, win.size = 2500) # peaksToBed(object = cds, file = "peaks.bed", gene.associated.peaks = TRUE)