ChIPpeakAnno to find peaks nearest to miRNA
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xyang2 ▴ 120
@xyang2-4387
Last seen 10 months ago
Hi, Jianrong, Do you think I can use ChIPpeakAnno to get both sided genes for a peak region? If so, how do you suggest, using both the TSS and TTS, or use both the 5UTR and 3UTR? Thanks a lot, Holly
ChIPpeakAnno ChIPpeakAnno • 671 views
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jun.yu • 0
@junyu-9556
Last seen 4.4 years ago

xyang2,

There is a new function calledĀ annoPeaks() in ChIPpeakAnno now.

annoPeaks (peaks, annoData, 
          bindingType=c("nearestBiDirectionalPromoters",
                        "startSite", "endSite", "fullRange"), 
          bindingRegion=c(-5000, 5000), 
          ignore.peak.strand=TRUE,
          select=c("all", "bestOne"),
          ...)

you can get the nearest upstream genes, and nearest downstream genes, then merge them.

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