filterOverlap {waveTiling} | R Documentation |
This function remaps the probe sequence to a reference sequence and filters probe sequence overlaps between PM and MM probes and/or between probes on the forward and reverse strand
filterOverlap(object, remap = TRUE, BSgenomeObject, chrId, strand = c("forward","reverse","both"), MM=FALSE, ...)
object |
object of class |
remap |
logical to determine whether the tiling array probe sequences have to be remapped to a more recent reference DNA sequence |
BSgenomeObject |
object of class |
chrId |
vector of numerics identifying the chromosomes for which the probes have to be filtered and/or remapped |
strand |
character indicating the strands for which the probes have to be filtered and/or remapped ( |
MM |
logical to indicate whether the tiling array contains MM probes or not |
... |
other arguments |
An object of class mapFilterProbe
is returned containing the indices of the filtered probes.
Kristof De Beuf <kristof.debeuf@ugent.be>
## Not run: data(leafdev) as(leafdev,"WaveTilingFeatureSet") library(BSgenome.Athaliana.TAIR.TAIR9) leafdevMapAndFilterTAIR9 <- filterOverlap(leafdev,remap=TRUE,BSgenomeObject=Athaliana,chrId=1:7,strand="both",MM=FALSE) ## End(Not run)