Question

ChIP seeker annotation error

1

Entering edit mode

Mar Mar ▴ 20

@mar-mar-23198

Last seen 3.2 years ago

Hello All,

I have differential binding sites boject obtain from diffBind (dba.report). I am using the ChIP Seeker package to annotate the peaks but keep getting the following error: Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’

Here is my peakset

BD

  seqnames              ranges strand |      Conc Conc_condition Conc_Control      Fold      p-value         FDR
               <Rle>           <IRanges>  <Rle> | <numeric>     <numeric>    <numeric> <numeric>    <numeric>   <numeric>
    [1] NC_000003.12   75668856-75670016      * |  12.27197    12.8243533      0.76175  12.06260 1.43013e-102 1.41852e-97
    [2] NC_000024.10   11320736-11323578      * |  10.58988    11.1419124      0.76175  10.38016 1.15927e-100 5.74930e-96
    [3] NC_000004.12         37431-38634      * |   6.42233     0.0596816      8.06241  -8.00273  6.67673e-98 2.20750e-93
    [4] NC_000017.11   21678164-21686752      * |   9.26507     9.8163416      0.76175   9.05459  3.54723e-95 8.79607e-91
    [5] NC_000022.11   12692637-12694102      * |   9.64945    10.2010195      0.76175   9.43927  2.35838e-87 4.67845e-83
    ...          ...                 ...    ... .       ...           ...          ...       ...          ...         ...
  [226] NC_000004.12 131722954-131744030      * |   11.8156      12.36301     5.337173   7.02584  2.54289e-17 4.78151e-16
  [227] NC_000015.10   68134159-68136364      * |    8.2514       8.80099     0.969455   7.83153  2.28289e-16 3.73532e-15
  [228] NC_000005.10   34189082-34194027      * |   10.4671      11.01445     3.990668   7.02378  1.46745e-15 2.12829e-14
  [229] NC_000018.10       108003-108613      * |   11.2783       5.46414    12.912836  -7.44869  3.68643e-12 3.26794e-11
  [230] NC_000004.12   49709306-49710113      * |   12.0662       6.40350    13.698765  -7.29526  1.23922e-08 6.37694e-0

peakAnno <- annotatePeak(BD, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")
> peakAnno <- annotatePeak(BD, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")
>> preparing features information...         2020-11-12 01:08:37 PM 
>> identifying nearest features...       2020-11-12 01:08:37 PM 
>> calculating distance from peak to TSS...  2020-11-12 01:08:38 PM 
>> assigning genomic annotation...       2020-11-12 01:08:38 PM 
Error in (function (classes, fdef, mtable)  : 
  unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’

I used diffloop package to add chr to the chromosome column but it did not work. Result in the same error.

Please let me know if you have any idea how to fix it. Highly appreciated.

DiffBind chipseq ChIPseeker ChipDb annotation • 2.4k views

ADD COMMENT • link 3.4 years ago • updated 3.2 years ago Mar Mar ▴ 20

0

Entering edit mode

Were you able to find a solution? I have this exact issue. Are you using the hg38 reference?

ADD REPLY • link 3.3 years ago Jasmine • 0

1

Entering edit mode

Yes,

I changed the seq level:

newnames <- paste0(c("1","2","3","4", "5","6","7", "8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X","Y","MT"))

names(newnames) <- paste0(c("NC_000001.11","NC_000002.12","NC_000003.12","NC_000004.12", "NC_000005.10","NC_000006.12","NC_000007.14", "NC_000008.11","NC_000009.12","NC_000010.11","NC_000011.10","NC_000012.12","NC_000013.11","NC_000014.9","NC_000015.10","NC_000016.10","NC_000017.11","NC_000018.10","NC_000019.10","NC_000020.11","NC_000021.9","NC_000022.11","NC_000023.11","NC_000024.10","NC_012920.1"))

peaks_with_new_seq_level <- renameSeqlevels(peaks_with_old_seq_level,newnames)

ADD REPLY • link 3.2 years ago Mar Mar ▴ 20