No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package
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@marcinkosinski-8570
Last seen 3.3 years ago
Poland

I am trying to perfom Chip-Seq Analysis which is greatly described in that conversation: http://biology.stackexchange.com/questions/16701/introduction-to-chip-seq . 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](http://bioconductor.org/packages/release/bioc/vignettes/ChIPpeakAnno/inst/doc/ChIPpeakAnno.pdf) `R` package from [Bioconductor](http://bioconductor.org/packages/release/bioc/html/ChIPpeakAnno.html). 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(org.Hs.eg.db)
    > macs.anno <- addGeneIDs(annotatedPeak=macs.anno,
    +                                                 orgAnn="org.Hs.eg.db",
    +                                                 IDs2Add="symbol")
    >
    > # no annotations for some genes
    > as.character(head(as.data.frame(macs.anno)$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.
 

chippeakanno chipseq annotation • 599 views
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