Error while annotating with Chipseeker
0
0
Entering edit mode
hamaor • 0
@hamaor-9799
Last seen 5.2 years ago

I followd the Diffbind pipeline for a ChipSeq data:

peaksets2 = dba(sampleSheet="SampleSheet.csv",config = data.frame(RunParallel=TRUE, AnalysisMethod=DBA_DESEQ2, bCorPlot=FALSE, bUsePval=TRUE, minQCth=10),minOverlap = 2)

peaksets2 <- dba.count(peaksets2)
peaksets2 <- dba.contrast(peaksets2, categories=DBA_FACTOR)
peaksets2 <- dba.analyze(peaksets2,bCorPlot=FALSE)

than I tried to annotate the peaks with Chipseeker:

txdb <- TxDb.Hsapiens.UCSC.hg19.knownGene
peakAnno_inAll = annotatePeak(peaksets2.DB, TxDb=txdb, annoDb = "org.Hs.eg.db", level = "gene")

but I keep get the same error:

> peakAnno_inAll = annotatePeak(peaksets2.DB, TxDb=txdb, annoDb = "org.Hs.eg.db", level = "gene")
>> preparing features information...         2019-02-25 14:26:15 
>> identifying nearest features...       2019-02-25 14:26:15 
>> calculating distance from peak to TSS...  2019-02-25 14:26:15 
>> assigning genomic annotation...       2019-02-25 14:26:15 
Error in `[<-.data.frame`(`*tmp*`, tssIndex, "Promoter", value = TRUE) : 
  replacement has 1 row, data has 0
In addition: Warning messages:
1: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
2: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
3: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
4: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)
5: In .Seqinfo.mergexy(x, y) :
  The 2 combined objects have no sequence levels in common. (Use
  suppressWarnings() to suppress this warning.)

what do I do wrong?

annotation chipseq • 1.1k views
ADD COMMENT

Login before adding your answer.

Traffic: 657 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6