peaksToBed {transcriptR} | R Documentation

## peaksToBed

### Description

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.

### Usage

    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)

### Arguments

`object` | A `ChipDataSet` object.
`file` | `Character`. A file name.
`strand.pred.color` | `Character`. A vector of length four, specifying colors of the predicted peak strand. The order of colors corresponds to 1) plus strand, 2) minus strand, 3) bideractional, 4) strand not determined. Default: c("blue", "red", "green4", "black").
`gene.associated.peaks` | `Logical`. Whether to return gene associated peaks (based on the prediction) only. Default: TRUE

### Value

A file in the BED format.

### Author(s)

Armen R. Karapetyan

### See Also

`constructCDS` `predictTssOverlap` `predictStrand` UCSC genome browser BED

### Examples

    ### 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)

[Package transcriptR version 1.12.0 Index]