No genes' ID in peak annotations during ChiP-Seq with ChIPpeakAnno R package
0
0
Entering edit mode
@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