How to query a set of genes in ChIPSeq data-in ChiPSeeker/ClusterProfiler?
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10 months ago

Hi, I am using Chipseeker and clusterprofiler to query a set of genes (about 100-200 genes) for TF binding sites 3k up or downstream of TSS. The code in vignette says the following

promoter <- getPromoters(TxDb=txdb, upstream=3000, downstream=3000) tagMatrix <- getTagMatrix(peak, windows=promoter)

But this code is for all TSS across genome. I want to get results for only a subset of genes (a simplified list is below) How should I modify this code to query a set of genes, say 10 genes for example TP53 TP63 TP73 DNMT1 DNMT3L FOXM1 BCL2 BAX BIM PIM1

Could anyone or Guangchuang Yu can help? Your help is much appreciated. Thanks in advance. Best regards, Jinesh.

R ChIP-Seq gene • 215 views
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