exportCherList: Function to export cherList into a file

In Ringo: R Investigation of ChIP-chip Oligoarrays

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)

Ringo documentation built on Nov. 8, 2020, 5:34 p.m.