Question: ChiPpeakAnno - using selfmade annotation
0
gravatar for florian.noack
4.6 years ago by
Germany
florian.noack0 wrote:

Hi everybody,

Iam using ChiPpeakAnnotation to annotate my MeDip-seq people and i works great so far using the premade annotations from ensemble (TSS, Exon ...). However now I would like to annotate peaks with a specific set of genes. To make my costume annotation I picked all genes which iam interested in from the premade TSS ensemble annotation and made a bed file (Name, Chr, Start, Ende). The following script i used to annotated the peaks:

mydata.ranged<-BED2RangedData("hmedip_allpeaks.bed",header=FALSE)

annoTSS<-BED2RangedData("switchgenesTSS.bed",header=F)

TSS <- annotatePeakInBatch(mydata.ranged, AnnotationData=annoTSS, output="both", multiple=T, maxgap= 100, PeakLocForDistance= "middle")

temp = as.data.frame(TSS)
pdf("TSS.pdf")
pie(table(temp [as.character(temp$fromOverlappingOrNearest) == "Overlapping" | (as.character(temp$fromOverlappingOrNearest) == "NearestStart" & !temp$peak %in% temp[as.character(temp$fromOverlappingOrNearest) == "Overlapping",]$peak),]$insideFeature))
dev.off()

The problem is that for all my different samples the the pie-chart looks the same which made me a bit suspicious. I think something is wrong with my costume made annotation right now the rangedData file looks like this: 

RangedData with 410 rows and 2 value columns across 20 spaces
                      space                 ranges   |      strand     score
                   <factor>              <IRanges>   | <character> <numeric>
ENSMUSG00000048960        1   [10993465, 11303682]   |           +         1
ENSMUSG00000025932        1   [14168954, 14310200]   |           +         1
ENSMUSG00000037509        1   [34678188, 34813309]   |           +         1
ENSMUSG00000026109        1   [50900647, 51187270]   |           +         1
ENSMUSG00000025978        1   [55170159, 55226782]   |           +         1

....

Should be sufficient the annotation of my peaks right ?

 

Thanks for any suggestions.

chip-seq • 1.4k views
ADD COMMENTlink modified 16 months ago by Biostar ♦♦ 20 • written 4.6 years ago by florian.noack0
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