ChIPseeker Error: Attempting to annotatePeaks

Question

[Vov]

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?

Answer 1

[Guangchuang Yu]

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).