User: shaunmwebb

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shaunmwebb0
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Posts by shaunmwebb

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Comment: C: significance of ChIPseq peak overlap
... I also can't get pool=F to work when using granges, I think this is because targetFiles[i] is used as input recursively rather than target.gr[[i]]? > enrichPeakOverlap(t.gr,list(t.gr,t2.gr),TxDb = txdb,nShuffle = 100,verbose = T,pool=F) Error in file.exists(dir) : invalid 'file' argument   ...
written 18 months ago by shaunmwebb0
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Comment: C: significance of ChIPseq peak overlap
... Hi, did you ever find a solution to this? I have the same problem, I am always getting the same p-values which is essentially just nshuffle/(nshuffle+1). I have a simple test case below: > t.gr<-GRanges(seqnames = "chr1",ranges = IRanges(start=seq(1,1000000,1000),width = 100),strand = "+") ...
written 18 months ago by shaunmwebb0

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