Question: ChIPseeker Error: Attempting to annotatePeaks
0
gravatar for cguzman.roma
4.0 years ago by
United States
cguzman.roma0 wrote:

Hello everyone,

I am attempting to annotate some ChIP-Seq data that I have called using MACS2. The output of MACS2 is .narrowPeak format.

I was able to successfully convert my ChIP Seq data to GRanges using:

peakstoanno = readPeakFile(file.path("/home/carlos/data/Sample_Pol-II-Chip/Peaks/narrow/Pol-II-Chip.MACS2_peaks.narrowPeak"), as="GRanges")

and then when I used the print(peakstoanno) function which returns:

I think attempted to run the command seen in the screenshot:

peaksAnno = annotatePeak(peakstoanno, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")

and received the following error:

> preparing features information...         2015-10-14 10:10:38 AM
Error in unlist(metadata(TXDB)) :
  error in evaluating the argument 'x' in selecting a method for function 'unlist': Error in sqliteSendQuery(con, statement, bind.data) :
  expired SQLiteConnection

I've already tried searching the error and only three search results came up, one being from this forum, but none solved the problem in anyway that helps me. (I am not using the developmental version of R).

Any ideas?

chipseeker software error • 789 views
ADD COMMENTlink modified 4.0 years ago by Guangchuang Yu1.1k • written 4.0 years ago by cguzman.roma0
Answer: ChIPseeker Error: Attempting to annotatePeaks
1
gravatar for Guangchuang Yu
4.0 years ago by
Guangchuang Yu1.1k
China/Guangzhou/Southern Medical University
Guangchuang Yu1.1k wrote:

1. by="exon" is currently not supported, and will be supported in next release, see C: ChIPseeker question: enrichPeakOverlap to find enrichment of genomic annotations

 

2. see https://github.com/GuangchuangYu/ChIPseeker/issues/13

ADD COMMENTlink written 4.0 years ago by Guangchuang Yu1.1k

1. Thank you, am looking forward to this. It is also possible add a by="intron" as well? I'm not sure how much more difficult this would be. This would greatly reduce the headaches for my current research.

2. Fixed. Thank you!

ADD REPLYlink modified 4.0 years ago • written 4.0 years ago by cguzman.roma0

duplicated, see A: ChIPseeker: Is it possible to create heatmaps / metagene plots without being cen

 

ADD REPLYlink written 4.0 years ago by Guangchuang Yu1.1k
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