Comparison of ChIPseeker and GREAT peak annotations
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11 months ago
MS ▴ 30

Hi,

I want to compare ChIPseeker and GREAT peak annotations.

I want to include "Two nearest genes" parameter that exists in GREAT to ChIPseeker script.

I used the parameters given below for ChIPseeker annotation according to tutorai but dont know how to interpret "Two nearest genes" parameter to this code.

Thank you.

peak <- readPeakFile(samplefiles[[3]])
peak


# Assign annotation db
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene

# Get annotations
peakAnnoList <- lapply(samplefiles, annotatePeak, TxDb=txdb, 
                       tssRegion=c(-1000, 1000), verbose=FALSE)
Peak annotation GREAT ChIPseeker • 298 views
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