Question: error running Chipseeker
0
gravatar for bdk
5.2 years ago by
bdk0
United States
bdk0 wrote:
Loading required package: IRanges
Loading required package: GenomeInfoDb
> med1 = read.delim("Mediator1.macs2_peaks.xls", skip = 25, header = TRUE)
> head(med1)
   chr   start     end length abs_summit pileup X.log10.pvalue. fold_enrichment
1 chr1 3295813 3296012    200    3295920     16         3.08787         2.15308
2 chr1 3511515 3511834    320    3511683     15         2.68170         2.02643
3 chr1 3699635 3699834    200    3699687     16         3.08787         2.15308
4 chr1 3701053 3701252    200    3701168     16         3.08787         2.15308
5 chr1 3851760 3851971    212    3851944     15         1.65003         1.59714
6 chr1 3883369 3883640    272    3883534     21         5.44513         2.78634
  X.log10.qvalue.                   name
1              -1 Mediator1.macs2_peak_1
2              -1 Mediator1.macs2_peak_2
3              -1 Mediator1.macs2_peak_3
4              -1 Mediator1.macs2_peak_4
5              -1 Mediator1.macs2_peak_5
6              -1 Mediator1.macs2_peak_6
> med1gr = GRanges(med1$chr,IRanges(med1$start, med1$end, med1$length ),height = med1$pileup,enrichment = med1$fold_enrichment)
> library(ChIPseeker)
> library(clusterProfiler)

library(TxDb.Mmusculus.UCSC.mm10.knownGene)
> txdb = TxDb.Mmusculus.UCSC.mm10.knownGene
> med1_anno <- annotatePeak(med1gr, tssRegion = c(-3000,3000), as = "GRanges", TranscriptDb = txdb, annoDb = "org.Mm.eg.db")
>> preparing features information...             2014-09-22 08:36:01 AM
>> identifying nearest features...               2014-09-22 08:36:02 AM
Error in IRanges:::normalizeSingleBracketSubscript(i, x) :
  subscript contains NAs or out of bounds indices

 

 

I was trying to extract features using ChIPseeker package. But I am getting error as shown above. I donot have any NA in file. I donot know why I am getting this error. any suggestion in this regard. I am biologist so least technical answer with some ready made recipe will be helpful.

Thanks

Bony

annotation chipseeker • 874 views
ADD COMMENTlink modified 5.2 years ago by Martin Morgan ♦♦ 24k • written 5.2 years ago by bdk0
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