Question: No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package
gravatar for MarcinKosinski
5.0 years ago by
MarcinKosinski10 wrote:

I am trying to perfom Chip-Seq Analysis which is greatly described in that conversation: . The same as autor of mentioned question I am a student of Applied Mathematics and I am doing my best to enter bioinformatics fields.

I am basically at the moment where I would like to annotate peaks with genes' IDs. To do this I am using [ChIPpeakAnno]( `R` package from [Bioconductor]( I used below  code to annotate my reads (outputs from `MACS`) with genes' ID's

    > library(ChIPpeakAnno)
    > # data(package = "ChIPpeakAnno")$results[,3]
    > macsOutput <- toGRanges(data="example_peaks.bed",
    +                                                 format = "MACS")

    > data(TSS.human.GRCh37)
    > macs.anno <- annotatePeakInBatch(macsOutput,
    +                                                                  AnnotationData=TSS.human.GRCh37,
    +                                                                  output="overlapping", maxgap=5000L)
    > library(
    > macs.anno <- addGeneIDs(annotatedPeak=macs.anno,
    +                                                 orgAnn="",
    +                                                 IDs2Add="symbol")
    > # no annotations for some genes
    > as.character(head($symbol))
    [1] "PTCHD2" "PTCHD2" "PTGER3" NA       "HFM1"   NA  

**but there occures that there are no genes' annotations for some peaks**. Can anyone tell me why this might happen? And how to avoid this? Does this refer to the `maxgap=5000L` parameter? When creating output from `MACS` I set a parameter for length to be 10 000.

chip-seq annotation • 1.7k views
ADD COMMENTlink modified 2.4 years ago by Biostar ♦♦ 20 • written 5.0 years ago by MarcinKosinski10
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