How to use EnsDb in annotatePeak from package "ChIPseeker"
1
1
Entering edit mode
foehn ▴ 80
@foehn-16281
Last seen 8 months ago
United States

Hello,

I'm trying to use EnsDb.Hsapiens.v86 as the annotation database for function annotatePeak from package "ChIPseeker". Yet I met a problem that the argument TxDb doesn't accept an EnsDb object:

library(EnsDb.Hsapiens.v86)
library(ChIPseeker)
EnsHg38 <- EnsDb.Hsapiens.v86
seqlevelsStyle(EnsHg38) <- "UCSC"

> peaks
GRanges object with 10 ranges and 0 metadata columns:
       seqnames                 ranges strand
          <Rle>              <IRanges>  <Rle>
   [1]    chr15 [ 22664756,  22664905]      *
   [2]    chr16 [ 66483816,  66483965]      *
   [3]     chr9 [135561956, 135562105]      *
   [4]    chr14 [ 88163786,  88163935]      *
   [5]    chr20 [ 57498528,  57498677]      *
   [6]    chr19 [ 49097916,  49098065]      *
   [7]    chr10 [ 89374396,  89374545]      *
   [8]     chr6 [  4589811,   4589960]      *
   [9]     chr6 [134420636, 134420785]      *
  [10]     chr1 [173499905, 173500054]      *
  -------
  seqinfo: 25 sequences (1 circular) from hg38 genome

res <- annotatePeak(peaks, TxDb = EnsHg38) 
>> preparing features information...             2019-02-15 14:22:12 
>> identifying nearest features...               2019-02-15 14:22:12 
>> calculating distance from peak to TSS...      2019-02-15 14:22:13 
>> assigning genomic annotation...               2019-02-15 14:22:13 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function 'intronsByTranscript' for signature '"EnsDb"'
In addition: Warning message:
In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

I wonder if it is possible to use EnsDb instead of TxDb in annotatePeak? Thanks.

GRanges ChIPseeker annotatePeak TxDb EnsDb • 868 views
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Entering edit mode
Johannes Rainer ★ 1.9k
@johannes-rainer-6987
Last seen 8 days ago
Italy

The reason is that ensembldb doesn't have an intronsByTranscript method. I'll add that and it should work.

cheers, jo

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intronsByTranscript is exported in ensembldb version 2.6.6 which will be available in a few days.

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