Question: custom annotation in annotatePeak
0
gravatar for andrew.gehrke
20 months ago by
andrew.gehrke0 wrote:

Hi Guangchuang,

Is there a way to control annotations in the the annotatePeak function?  For instance I would like to ignore "downstream" and consider those peaks "intergenic".  Or for instance combine "1st exon" with "other exon" so there is one category of "exon".  

Any help would be great, thanks for doing this!

-Andrew

chipseeker guangchuang yu • 598 views
ADD COMMENTlink modified 20 months ago • written 20 months ago by andrew.gehrke0
Answer: custom annotation in annotatePeak
0
gravatar for Guangchuang Yu
20 months ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:
> require(ChIPseeker)
Loading required package: ChIPseeker

ChIPseeker v1.15.3  For help: https://guangchuangyu.github.io/ChIPseeker

If you use ChIPseeker in published research, please cite:
Guangchuang Yu, Li-Gen Wang, Qing-Yu He. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization. Bioinformatics 2015, 31(14):2382-2383
> ff = getSampleFiles()[[4]]
> options(ChIPseeker.ignore_1st_exon = TRUE)
> options(ChIPseeker.ignore_1st_intron = TRUE)
> options(ChIPseeker.ignore_downstream = TRUE)
> options(ChIPseeker.ignore_promoter_subcategory = TRUE)
> x = annotatePeak(ff)
>> loading peak file...                 2018-01-09 11:36:33
>> preparing features information...         2018-01-09 11:36:33
>> identifying nearest features...         2018-01-09 11:36:34
>> calculating distance from peak to TSS...     2018-01-09 11:36:34
>> assigning genomic annotation...         2018-01-09 11:36:34
>> assigning chromosome lengths             2018-01-09 11:36:52
>> done...                     2018-01-09 11:36:52
Warning message:
In loadTxDb(TxDb) :
  >> TxDb is not specified, use 'TxDb.Hsapiens.UCSC.hg19.knownGene' by default...
> x
Annotated peaks generated by ChIPseeker
1331/1331  peaks were annotated
Genomic Annotation Summary:
     Feature  Frequency
6   Promoter 58.7528174
2     5' UTR  0.3005259
1     3' UTR  2.1036814
3       Exon  3.0052592
5     Intron  7.9639369
4 Intergenic 27.8737791

In github version, you can do it via options. Beware that annotatePeak always output detail annotations and such options only work for summarizing the result and visualization.

ADD COMMENTlink written 20 months ago by Guangchuang Yu1.1k
Answer: custom annotation in annotatePeak
0
gravatar for andrew.gehrke
20 months ago by
andrew.gehrke0 wrote:

Thank you for the quick response! Everything working great I appreciate it!

-Andrew

ADD COMMENTlink modified 20 months ago • written 20 months ago by andrew.gehrke0
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