Unable to annotate the differential peaks from DiffBind using ChIPseeker
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researcher • 0
@researcher-20723
Last seen 22 months ago

I am using ChIPseeker to annotate my differential peaks but getting an error:

Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’

I don't have any clue to solve this error. Any suggestion is highly appreciated.

Following are my commands :

   dba.show(DBdata_count_contrast_DESeq2)


ID Condition Caller Intervals FRiP
1  C1_2485        C1 counts    108125 0.16
2  C1_3923        C1 counts    108125 0.61
3  C4_2753        C4 counts    108125 0.34
4  C4_1274        C4 counts    108125 0.44
5  C4_4133        C4 counts    108125 0.15
6  C4_4205        C4 counts    108125 0.48
7  C4_4206        C4 counts    108125 0.55
8  C4_4750        C4 counts    108125 0.44
9  C4_1602        C4 counts    108125 0.28
10 C4_1877        C4 counts    108125 0.20
11 C4_3012        C4 counts    108125 0.42
12 C4_3593        C4 counts    108125 0.16
13 C4_3672        C4 counts    108125 0.58
14 C4_4748        C4 counts    108125 0.57
peaks.C1<- peaks.consensus[DBdata_count_contrast_DESeq2$called[,1]==1 & DBdata_count_contrast_DESeq2$called[,2]==1]


peaks.C4<- peaks.consensus[DBdata_count_contrast_DESeq2$called[,3]==1 & DBdata_count_contrast_DESeq2$called[,4]==1 & DBdata_count_contrast_DESeq2$called[,5]==1 & DBdata_count_contrast_DESeq2$called[,6]==1& DBdata_count_contrast_DESeq2$called[,7]==1 & DBdata_count_contrast_DESeq2$called[,8]==1 & DBdata_count_contrast_DESeq2$called[,9]==1 & DBdata_count_contrast_DESeq2$called[,10]==1 & DBdata_count_contrast_DESeq2$called[,11]==1 & DBdata_count_contrast_DESeq2$called[,12]==1 & DBdata_count_contrast_DESeq2$called[,13]==1 & DBdata_count_contrast_DESeq2$called[,14]==1]

peaks.C1_ann<-annotatePeak(peaks.C1, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")

preparing features information... 2019-09-13 11:34:44 identifying nearest features... 2019-09-13 11:34:45 calculating distance from peak to TSS... 2019-09-13 11:34:45 assigning genomic annotation... 2019-09-13 11:34:45 adding gene annotation... 2019-09-13 11:34:58 'select()' returned 1:many mapping between keys and columns assigning chromosome lengths 2019-09-13 11:34:58 done... 2019-09-13 11:34:58

peaks.C4_ann<-annotatePeak(peaks.C4, tssRegion=c(-3000, 3000), TxDb=txdb, annoDb="org.Hs.eg.db")

preparing features information... 2019-09-13 11:35:11 identifying nearest features... 2019-09-13 11:35:11 Error in (function (classes, fdef, mtable) : unable to find an inherited method for function ‘NSBS’ for signature ‘"SortedByQueryHits"’

chip seq ChIPseeker peak annotation annotatePeak() Diffbind • 1.9k views
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Entering edit mode

I think this may stil be the chr issue. try installing diffloop package

dbobject <- addchr(dbobject) and then re-run the annotatedPeak()

be careful, you have to use thee addchr() only once, as it will keep adding chr to the chromosome column.

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Entering edit mode

Adding chr before the chromosome numbers fixed this issue. Thank you!

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