ChIPseeker peak annotation tssRegion
2
0
Entering edit mode
@lifengliubiology-13766
Last seen 3.6 years ago

I was confused about the argument of tssRegion in peak annotation function of ChIPseeker. It seems that there is no change of the annotation output when I changed the tssRegion setting, from tssRegion=c(-3000, 3000) to tssRegion=c(-2000, 0). I am working on a plant species, Brachypodium distachyon (~272 Mb). I thought this is to define the promoter region, which supposed to be upstream of TSS or 5UTR and setting upstream=3000, downstream=3000 is just for plotting around TSS. So, what is the point of this argument here?

And, does anyone know how the promoter was defined in genomic annotation categories (promoter, 5/3 UTR, exon, intron, downstream, intergenic)? For downstream, does it start after 3' UTR? Can I manually set the downstream range, e.g. 500bp?

peakAnno <- annotatePeak(files[[4]], tssRegion=c(-3000, 3000), TxDb=txdb)

Thanks

chipseeker annotation chipseq • 1.2k views
ADD COMMENT
1
Entering edit mode
Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

do you have any reproducible example of change the `tssRegion` setting has no effect of the result?

ADD COMMENT
0
Entering edit mode

R script used here:

library(GenomicFeatures)

library(ChIPseeker)

library(clusterProfiler)

txdb <- loadDb("Bdistachyon_v314.sqlite")
file_H3K27me3="H3K27me3_DiffBind_Peaks.bed"
peak_H3K27me3 <- readPeakFile(file_H3K27me3)

peakAnno <- annotatePeak(peak_H3K27me3, tssRegion=c(-3000, 3000), TxDb=txdb, genomicAnnotationPriority = c( "5UTR",  "Exon", "Intron", "3UTR", "Promoter", "Downstream","Intergenic"))

pdf("H3K27me3_AnnoPie_U3000_D3000.pdf")
plotAnnoPie(peakAnno)
dev.off()

pdf("H3K27me3_AnnoUpset_U3000_D3000.pdf")
upsetplot(peakAnno, sets.bar.color="grey23", matrix.color = "black", main.bar.color = "grey23")
dev.off()

write.csv(peakAnno, "H3K27me3_all_peaks_annotation_U3000_D3000.csv")

peakAnno <- annotatePeak(peak_H3K27me3, tssRegion=c(-2000, 0), TxDb=txdb, genomicAnnotationPriority = c( "5UTR",  "Exon", "Intron", "3UTR", "Promoter", "Downstream","Intergenic"))

pdf("H3K27me3_AnnoPie_U2000_D0.pdf")
plotAnnoPie(peakAnno)
dev.off()

pdf("H3K27me3_AnnoUpset_U2000_D0.pdf")
upsetplot(peakAnno, sets.bar.color="grey23", matrix.color = "black", main.bar.color = "grey23")
dev.off()

write.csv(peakAnno, "H3K27me3_all_peaks_annotation_U2000_D0.csv")


lifengl-dm:scripts lifengliu$ diff H3K27me3_all_peaks_annotation_U2000_D0.csv H3K27me3_all_peaks_annotation_U3000_D3000.csv

lifengl-dm:scripts lifengliu$


And the numbers in AnnoPie or AnnoUpset are exactly the same. 

so the tssRegion argument here is to define the promoter region or something else? If you need the bed file and txdb file, I can send them to you.

ADD REPLY
1
Entering edit mode
@lifengliubiology-13766
Last seen 3.6 years ago

Figured it out. The problem is the priority of the genomic annotation. Using the priority of ​genomicAnnotationPriority = c( "5UTR",  "Exon", "Intron", "3UTR", "Promoter", "Downstream","Intergenic") gives me same result with tssRegion=c(-3000, 3000)​ or tssRegion=c(-2000, 0)​. But if I change it to genomicAnnotationPriority = c( "Promoter", "5UTR",  "Exon", "Intron", "3UTR",  "Downstream","Intergenic"), it gives me quite different annotation and the annotation (genomicAnnotationPriority = c( "Promoter", "5UTR",  "Exon", "Intron", "3UTR",  "Downstream","Intergenic"), tssRegion=c(-2000, 0)​​) makes more sense in my case. 

ADD COMMENT

Login before adding your answer.

Traffic: 348 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6