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Mar Mar
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@mar-mar-23198
Last seen 3.8 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.
Were you able to find a solution? I have this exact issue. Are you using the hg38 reference?
Yes,
I changed the seq level:
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)