Question: ChIPseeker annotatePeak definition
0
gravatar for C T
3.3 years ago by
C T90
United States
C T90 wrote:

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 • 900 views
ADD COMMENTlink modified 3.3 years ago by Guangchuang Yu1.1k • written 3.3 years ago by C T90
Answer: ChIPseeker annotatePeak definition
0
gravatar for Guangchuang Yu
3.3 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

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.

 

 

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Guangchuang Yu1.1k

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?

ADD REPLYlink written 3.3 years ago by C T90
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 361 users visited in the last hour