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Question: ChIPpeakAnno to find peaks nearest to miRNA
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gravatar for xyang2
4.9 years ago by
xyang2120
xyang2120 wrote:
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
ADD COMMENTlink modified 26 days ago by jun.yu0 • written 4.9 years ago by xyang2120
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gravatar for jun.yu
26 days ago by
jun.yu0
jun.yu0 wrote:

xyang2,

There is a new function called 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.

ADD COMMENTlink written 26 days ago by jun.yu0
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