Currently I am doing an analysis where it is required to annotate 100kb region. It is DNA-sequencing data. I used the ChIPpeakAnno tool to annotate it. I have the following question.
Can anyone suggest me how does the tool assign the 100kb region into the promoter region. I know the distance is calculated from TSS. However, I do not understand how was the promoter region assigned to 100kb regions? I have the sample file attached here.
I used the following function in r to do the annotation
Code should be placed in three backticks as shown below
overlaps.anno <- annotatePeakInBatch(gr3, AnnotationData=annoData , output="both") aCR<-assignChromosomeRegion(gr3, nucleotideLevel=FALSE, precedence=c("Promoters", "immediateDownstream", "fiveUTRs", "threeUTRs", "Exons", "Introns"), TxDb=TxDb.Hsapiens.UCSC.hg19.knownGene) # include your problematic code here with any corresponding output # please also include the results of running the following in an R session sessionInfo( )