ChIPseeker annotatePeak definition
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C T ▴ 140
@c-t-5858
Last seen 10 months ago
United States

Hi, I am wondering how I can find the exact definition used to do peak annotation when doing:

peakAnno <- annotatePeak(peaks, tssRegion=c(-5000, 5000),
                         TxDb=txdb, annoDb="org.Hs.eg.db")

For example: I know downstream is within 3kb from the gene but is it from end of gene or start of gene? etc.

If it is from org.Hs.eg.db can you let me know how I can find that out?

Thanks

Lin 

chipseeker • 2.3k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 6 months ago
China/Guangzhou/Southern Medical Univer…

RTFM:

downstream is the downstream of gene end which was documented in vignette.

annoDb is used to convert gene ID which was also documented in vignette.

 

 

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Thanks for your reply. Sorry. which vignette were you referring to? this one http://bioconductor.org/packages/release/bioc/vignettes/ChIPseeker/inst/doc/ChIPseeker.html ?

What about distal intergenic?

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