Question

ChIPpeakAnno to find peaks nearest to miRNA

0

Entering edit mode

xyang2 ▴ 120

@xyang2-4387

Last seen 4.1 years 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 • 1.3k views

ADD COMMENT • link updated 7.2 years ago by jun.yu • 0 • written 12.0 years ago by xyang2 ▴ 120

score 0 · Answer 1 · 2017-10-25

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.