YuLab-SMU
Peak Annotations
Hi I have a peak file p1. I annotate files peakAnno <- annotatePeak(p1,tssRegion=c(-3000, 3000),TxDb=txdb, annoDb="org.Hs.eg.db") features = attributes(peakAnno)
I looked at head(features['detailGenomicAnnotation'][[1]]) for every peak it has multiple columns true. Why? I want to know exactly, how do you assign promoter region to a peak.
If it was located within tssRegion=c(-3000, 3000), it will be assigned to promoter.
The detailGenomicAnnotation is only for internal use.
My question is when you get the TXDB object which has a list of annotated TSS.
How do you find the overlap of a peak with these regions? what is the min and maximum base pair overlap?
KG
On Mon, Nov 21, 2016 at 8:41 PM, Guangchuang Yu [email protected] wrote:
If it was located within tssRegion=c(-3000, 3000), it will be assign to promoter.
— You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_GuangchuangYu_ChIPseeker_issues_43-23issuecomment-2D262123031&d=DQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=XW5NHlYxJyov09gidSvHlCx2roVNYW1IqPo7Rmin2pE&m=Mn05475yzKmMo9T0x8QnNjl3jzwNl7aC78RpzprrO5o&s=1QGgEHKF1TDCd8aoL0avNkiVRBlU6YYh1FNYik3tmGA&e=, or mute the thread https://urldefense.proofpoint.com/v2/url?u=https-3A__github.com_notifications_unsubscribe-2Dauth_ALk-2D7SwbdM8Wlss6XYXQ-2DWWKfOioU-2D3Kks5rAkgzgaJpZM4K4jBc&d=DQMCaQ&c=8hUWFZcy2Z-Za5rBPlktOQ&r=XW5NHlYxJyov09gidSvHlCx2roVNYW1IqPo7Rmin2pE&m=Mn05475yzKmMo9T0x8QnNjl3jzwNl7aC78RpzprrO5o&s=nPkySgnpqqr8L3ohvuAhY4ApFIIKOnaJZ_8gMnDuFZg&e= .
I am still confused with distancetoTSS values from annotation of peaks. if you allow minimum overlap of 1 bp.
There are 4 possibilites of overlaps of peak region with transcript region
- Overlapping start
- include-peak region is inside the transcript region
- include feature- has partial region overlap with transcript 4.overlapping end.
How do define distance to TSS in these 4 cases for both + and - strand of a transcript.
I though you were talking about the promoter annotation. If you are talking about the distanceToTSS, then they don't necessarily overlapping, see http://guangchuangyu.github.io/2014/10/multiple-annotation-in-chipseeker/.