exportCherList {Ringo} | R Documentation |
Function to export cherList into a file of gff or BED format. This files can be imported as tracks into genome browsers.
exportCherList(object, filename = "chers.gff", format = "gff3", ...)
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 |
... |
further arguments to be passed on to the trackSet
method |
First converts the cherList
into an object of class
trackSet
from package rtracklayer and then calls the
export
method as defined for a trackSet
.
returns invisible NULL; called for the side effect of writing the file
filename
.
Joern Toedling
Class trackset
in package rtracklayer
## 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)