Question: ChIPseeker Error: Attempting to annotatePeaks
1
gravatar for Vov
3.8 years ago by
Vov70
United States
Vov70 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?

error mypost chipseeker chip-seq • 1.8k views
ADD COMMENTlink modified 3.7 years ago by Guangchuang Yu2.2k • written 3.8 years ago by Vov70
0
gravatar for Guangchuang Yu
3.7 years ago by
Guangchuang Yu2.2k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.2k wrote:

1. You should use

readPeakFile(your_file, header=FALSE)

2. this is an known issue, see https://github.com/GuangchuangYu/ChIPseeker/issues/13 and was fixed in the current release (in BioC 3.2).

 

 

ADD COMMENTlink modified 3.7 years ago • written 3.7 years ago by Guangchuang Yu2.2k
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