Generate a custom annotation for ChIPQC
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Last seen 2.4 years ago
United States

Hi, I am trying to create a custom Chicken (galGal6) annotation for ChIPQC, but the only post that I could find didn't solve my problem How to generate custom annotation for rat genome rn6 in ChIPQC

I want to generate the Relative Enrichment of Genomic Intervals (REGI) graphs, and it always outputs this error

> plotRegi(chipObj)
Error: Faceting variables must have at least one value
Run `rlang::last_error()` to see where the error occurred.
In addition: Warning message:
In plotRegi(chipObj) : No genomic annotation computed

I just have no idea how to move forward from here...

What I used to generate my custom annotation is:

myNewGetAnnotation <- function(GeneAnnotation = "gga", AllChr){
  txdb <- TxDb.Ggallus.UCSC.galGal6.refGene
  All5utrs <- reduce(unique(unlist(fiveUTRsByTranscript(txdb))))
  All3utrs <- reduce(unique(unlist(threeUTRsByTranscript(txdb))))
  Allcds <- reduce(unique(unlist(cdsBy(txdb,"tx"))))
  Allintrons <- reduce(unique(unlist(intronsByTranscript(txdb))))
  Alltranscripts <- reduce(unique(transcripts(txdb)))

  posAllTranscripts <- Alltranscripts[strand(Alltranscripts) == "+"]
  posAllTranscripts <- posAllTranscripts[!(start(posAllTranscripts)-20000 < 0)]
  negAllTranscripts <- Alltranscripts[strand(Alltranscripts) == "-"]
  chrLimits <- seqlengths(negAllTranscripts)[as.character(seqnames(negAllTranscripts))]
  negAllTranscripts <- negAllTranscripts[!(end(negAllTranscripts)+20000 > chrLimits)]
  Alltranscripts <- c(posAllTranscripts,negAllTranscripts)
  Promoters500 <-  reduce(flank(Alltranscripts,500))
  Promoters2000to500 <-  reduce(flank(Promoters500,1500))
  LongPromoter20000to2000  <- reduce(flank(Promoters2000to500,18000))
  if(!missing(AllChr) & !is.null(AllChr)){
    All5utrs <- ChIPQC:::GetGRanges(All5utrs,AllChr=AllChr)
    All3utrs <- ChIPQC:::GetGRanges(All3utrs,AllChr=AllChr)
    Allcds <- ChIPQC:::GetGRanges(Allcds,AllChr=AllChr)
    Allintrons <- ChIPQC:::GetGRanges(Allintrons,AllChr=AllChr)
    Alltranscripts <- ChIPQC:::GetGRanges(Alltranscripts,AllChr=AllChr)
    Promoters500 <- ChIPQC:::GetGRanges(Promoters500,AllChr=AllChr)
    Promoters2000to500 <-  ChIPQC:::GetGRanges(Promoters2000to500,AllChr=AllChr)
    LongPromoter20000to2000  <- ChIPQC:::GetGRanges(LongPromoter20000to2000,AllChr=AllChr)

galGal6 <- myNewGetAnnotation(AllChr = "chr1") ##here, I also can't figure out how to include all chromosomes##

Please help..!

Thank you

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