Hi All, i have a list of differentially methylated regions (DMRs) and I am trying to get the distance of these particular DMRs to known TSS, so I am using the ChIPpeakAnno package from Bioconductor, the question is: Is able this package to get the nearest start to up and downstream genes. From what I see, the package displays only one NearestStart, probably the downstream one, I tried setting the parameters up with both, but I got apart from Nearest if it is overlapping or not.
I add my script
library(GenomicFeatures) library(ChIPpeakAnno) data(TSS.human.GRCh37) dmrs.ranges<-with(DMRs,RangedData(IRanges(start_DMR,end_DMR,names=id),space=space)) annotatedPeak <-annotatePeakInBatch(dmrs.ranges, AnnotationData =TSS.human.GRCh37,output="both") annotatedPeak<-as.data.frame(annotatedPeak)
I read somewhere that using precede function in GenomicRanges, is the point, but I don't know how to get it, Could anybody help me with this point?
Thanks in advance