exportCherList: 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

Value

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

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.

Examples

Run this code

## 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)