ChIPseeker error when I wnat to get tagMatrix
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hfyuan2016 • 0
@hfyuan2016-23538
Last seen 2.0 years ago

Hi, I want to use chipseeker package to annotate my ATAC-Seq peaks. but I get the error as below:

>library(GenomicFeatures)
>library(ChIPseeker)
> require(GenomicFeatures) 
>txdb <-  makeTxDbFromGFF("data/Aqu3.1_Gene.checked.gff3") 
>peak1 <-  readPeakFile("data/macs/1hps_1_peaks.narrowPeak")  
>promoter <-  getPromoters(TxDb = txdb, upstream = 3000, downstream = 3000)
> tagMatrix <- getTagMatrix(peak1, windows = promoter)
**>Error in getTagMatrix(peak1, windows = promoter) :    width of windows should be equal...**

then I checked the promoter and found that:

> promoter
 GRanges object with 0 ranges and 0 metadata columns:
   seqnames    ranges strand
      <Rle> <IRanges>  <Rle>
  -------
  seqinfo: 2349 sequences from an unspecified genome; no seqlengths

could anyone know what is wrong with this? Thanks very much!!!

Best Hf

Chipseeker TxDb getpromoters software error • 353 views
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