ChIPSeeker with Ensembl IDs
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Entering edit mode
Assa Yeroslaviz ★ 1.5k
@assa-yeroslaviz-1597
Last seen 27 days ago
Munich, Germany

I'm trying to run ChIPSeeker with annotation files from Ensembl, but it keep giving me an error.

I have changed the seqlevels to "UCSC" ( see below), but when running this command

peakAnno1 <- annotatePeak(peak = peak1, tssRegion=c(-3000, 3000), TxDb = edb)

I get the error

>> preparing features information...         2020-04-06 12:58:26 
>> identifying nearest features...       2020-04-06 12:58:26 
>> calculating distance from peak to TSS...  2020-04-06 12:58:28 
>> assigning genomic annotation...       2020-04-06 12:58:28 
Error in `[.data.frame`(nearestFeatures.df, , cn) : 
  undefined columns selectedError in `[.data.frame`(nearestFeatures.df, , cn) : undefined columns selected

I can't figure out which columns are looked for to debug the problem.

Any ideas, why this is happening? I habe also tried with and without the annoDb = "org.Mm.eg.db" or annoDb = "EnsDb.Mmusculus.v79"

thanks

Assa

> peak1
GRanges object with 202315 ranges and 6 metadata columns:
           seqnames              ranges strand |                      V4        V5       V6        V7        V8        V9
              <Rle>           <IRanges>  <Rle> |                <factor> <integer> <factor> <numeric> <numeric> <numeric>
       [1]     chr1     3261236-3261429      * |      H3K4m3_WK31_peak_1        10        .   2.71368   2.82763   1.05939
       [2]     chr1     3264207-3264630      * |      H3K4m3_WK31_peak_2        55        .    5.8844   8.00663   5.58589
       [3]     chr1     3339728-3339940      * |      H3K4m3_WK31_peak_3         0        .   1.87219   1.68288   0.08676
       [4]     chr1     3369422-3369611      * |      H3K4m3_WK31_peak_4        11        .   3.24958   2.88762   1.11099
       [5]     chr1     3469328-3469531      * |      H3K4m3_WK31_peak_5        21        .   3.66036   4.09408   2.14879
       ...      ...                 ...    ... .                     ...       ...      ...       ...       ...       ...
  [202311]     chrX 167635685-167636864      * | H3K4m3_WK31_peak_202311        28        .   3.99902   4.92286   2.89243
  [202312]     chrX 167641667-167642491      * | H3K4m3_WK31_peak_202312        17        .   3.34516   3.66866   1.78698
  [202313]     chrX 167647254-167647450      * | H3K4m3_WK31_peak_202313        10        .   3.03725   2.84692   1.07598
  [202314]     chrX 167648493-167650286      * | H3K4m3_WK31_peak_202314        10        .   2.93389    2.7888   1.03137
  [202315]     chrX 167651479-167651741      * | H3K4m3_WK31_peak_202315       106        .   8.56011  13.63289  10.61471
  -------
  seqinfo: 21 sequences from an unspecified genome; no seqlengths
> seqlevels(edb)
 [1] "chr1"                      "chr10"                     "chr11"                     "chr12"                    
 [5] "chr13"                     "chr14"                     "chr15"                     "chr16"                    
 [9] "chr17"                     "chr18"                     "chr19"                     "chr2"                     
[13] "chr3"                      "chr4"                      "chr5"                      "chr6"                     
[17] "chr7"                      "chr8"                      "chr9"                      "CHR_MG132_PATCH"          
[21] "CHR_MG153_PATCH"           "CHR_MG184_PATCH"           "CHR_MG3829_PATCH"          "CHR_MG3833_PATCH"         
[25] "CHR_MG4136_PATCH"          "CHR_MG4151_PATCH"          "CHR_MG4180_PATCH"          "CHR_MG4209_PATCH"         
[29] "CHR_MG4211_PATCH"          "CHR_MG4212_PATCH"          "CHR_MG4213_PATCH"          "CHR_MG4214_PATCH"         
[33] "CHR_MG4222_MG3908_PATCH"   "CHR_MG4237_PATCH"          "CHR_MMCHR1_CHORI29_IDD5_1" "GL456210.1"               
[37] "GL456211.1"                "GL456212.1"                "GL456216.1"                "GL456219.1"               
[41] "GL456221.1"                "GL456233.1"                "GL456239.1"                "GL456350.1"               
[45] "GL456354.1"                "GL456372.1"                "GL456381.1"                "GL456385.1"               
[49] "JH584292.1"                "JH584293.1"                "JH584294.1"                "JH584295.1"               
[53] "JH584296.1"                "JH584297.1"                "JH584298.1"                "JH584299.1"               
[57] "JH584303.1"                "JH584304.1"                "chrM"                      "chrX"                     
[61] "chrY"
chipseeker Ensembl EnsDb.Mmusculus.v79 ensembldb • 216 views
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Entering edit mode

Seems ChIPseeker does not support ensembldb EnsDb annotation databases - different/more columns are returned from EnsDb databases which results ultimately in the error message you see. I added a pull request to the ChIPseeker github repository which adds support for EnsDb databases to annotatePeak.

Until the code is merged into the ChIPseeker package you might try to install the my changed version with devtools::install_github("jorainer/ChIPseeker") and see if you still get the same error.

cheers, jo

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