exportCherList {Ringo} | R Documentation

## Function to export cherList into a file

### Description

Function to export cherList into a file of gff or BED format. This files can be imported as tracks into genome browsers.

### Usage

    exportCherList(object, filename = "chers.gff", format = "gff3",
                   genome="hg18", ...)

### Arguments

`object` | an object of class `cherList`
`filename` | character; path to file to be written
`format` | Format of exported file; currently only "gff3" and "bed" are supported
`genome` | character; which genome the ChIP-enriched regions were found in denoting species and assembly, e.g. ‘hg18’ or ‘mm9’
`...` | further arguments to be passed on to the `trackSet` method

### Details

First converts the `cherList` into an object of class `trackSet` from package rtracklayer and then calls the `export` method as defined for a `trackSet`.

### Value

returns invisible NULL; called for the side effect of writing the file `filename`.

### Author(s)

Joern Toedling

### See Also

Class `trackset` in package rtracklayer

### Examples

    ## Not run:
      exDir <- system.file("exData",package="Ringo")
      load(file.path(exDir,"exampleProbeAnno.rda"))
      load(file.path(exDir,"exampleX.rda"))
      smoothX <- computeRunningMedians(exampleX, probeAnno=exProbeAnno,
           modColumn = "Cy5", allChr = "9", winHalfSize = 400)
      chersX <- findChersOnSmoothed(smoothX, probeAnno=exProbeAnno,
           thresholds=0.45, allChr="9", distCutOff=600, cellType="human")
      exportCherList(chersX, file="chers.gff")

    ## End(Not run)

[Package Ringo version 1.48.0 Index]