ChIPseeker: covplot function: error with some ENCODE data sets
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@sarabusquets88-7655
Last seen 6.5 years ago
Netherlands

I am performing an exploratory analysis of the ENCODE Txn Factor ChiPseq data. For some reason that I cannot understand, the covplot function only works for certain input files. It works perfectly for certain input files but when I change just the input file and maintain the script the same I get the following error. All the files I want to analyze come from the ENCODE databse and are .narrowpeaks or .broadpeaks format. Then I transform them to a GRanges file to analyze them.

> covplot <- covplot(my_granges,weightCol ="score") #coverage plot

Error in data.frame(chr = names(cov[i]), start = start(x), end = end(x),  : 
  arguments imply differing number of rows: 1, 118, 119

For example, when I use the ENCODE ChiPseq data for BCL11A in hESC.narrowpeaks or BCL11A in hESC Replicate 1.broadpeaks it works, but when I use BCL11A in hESC Replicate2.broadpeaks, it does not work.

 

chiPseeker covplot ENCODE ChIpseq • 1.4k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

please post the link to download this encode dataset, I will have a look at it.

Bests,

Guangchuang
 

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wenhuo hu ▴ 200
@wenhuo-hu-5208
Last seen 3.4 years ago
United States

It works right now if this: install_github("GuangchuangYu/ChIPseeker") Thanks man.

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please cite this paper: http://www.ncbi.nlm.nih.gov/pubmed/25765347

 

Thanks.

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@sarabusquets88-7655
Last seen 6.5 years ago
Netherlands

Dear Guangchuang,

Thanks for your reply!

 - This is replicate 1 of BCL11A ChIPseq in hESC from ENCODE (the one that works): 

https://www.genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=424063059_EqT7VUHDesA7tH02ocEyI12cm5kE&g=wgEncodeHaibTfbsH1hescBcl11aPcr1xPkRep1

- This is replicate 2 of BCL11A ChIPseq in hESC from ENCODE (the one that does not work):

https://www.genome.ucsc.edu/cgi-bin/hgTrackUi?hgsid=424063059_EqT7VUHDesA7tH02ocEyI12cm5kE&g=wgEncodeHaibTfbsH1hescBcl11aV0416102PkRep2

You have to click on "metadata", and then the link to download the file will appear.

Thank you very much for looking into this!

 

Best,

 

Sara

 

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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months ago
China/Guangzhou/Southern Medical Univer…

Thanks for your report. It has been fixed in version >=1.4.1

Please wait 2-3 days for Bioconductor to update tarball.
 

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@sarabusquets88-7655
Last seen 6.5 years ago
Netherlands

Thank you very much!

It works perfectly!

 

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