I am trying to perfom Chip-Seq Analysis which is greatly described in that conversation: 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
R package from Bioconductor. I used below code to annotate my reads (outputs from
MACS) with genes' ID's
> library(ChIPpeakAnno) > # data(package = "ChIPpeakAnno")$results[,3] > macsOutput <- toGRanges(data="example_peaks.bed", + format = "MACS") > data(TSS.human.GRCh37) > macs.anno <- annotatePeakInBatch(macsOutput, + AnnotationData=TSS.human.GRCh37, + output="overlapping", maxgap=5000L) > library(org.Hs.eg.db) > macs.anno <- addGeneIDs(annotatedPeak=macs.anno, + orgAnn="org.Hs.eg.db", + IDs2Add="symbol") > > # no annotations for some genes > as.character(head(as.data.frame(macs.anno)$symbol))  "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.