missing function queryConsensusPeaks in Bioc v.2.10.0

[gaiatek]

Hi,

I am trying to follow the bioconductor vignette for ENCODEExplorer and when I try to obtain consensus Peaks from ChIP-Seq (section 5.1) I get the following error:

res = queryConsensusPeaks("22Rv1", "GRCh38", "CTCF")
Error in queryConsensusPeaks("22Rv1", "GRCh38", "CTCF"): 
  could not find function "queryConsensusPeaks"

It looks like the function is not part of the package anymore? I also looked into package ENCODExplorerData, but to no avail... Could you point me to the function? thanks!

session info:

• Session info -------------------------------------------------- setting value
  version R version 3.6.2 (2019-12-12) os Windows 10 x64
  system x86_64, mingw32
  ui RStudio
  language (EN)
  collate English_United States.1252
  ctype English_United States.1252
  tz America/New_York
  date 2020-02-16

• Packages ------------------------------------------------------ package version date lib source
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  ENCODExplorerData 0.99.1 2020-02-16 [1] Bioconductor
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[ericfournier2]

Hi,

I don't know about version ENCODExplorer version 2.10 (which probably was in BioConductor release 2.9), but the function is definitely in ENCODExplorer 2.12.1, the one in the current BioConductor release (Bioc 2.10). Is there a reason why you can't switch to that one?

Cheers, -Eric

[gaiatek]

Thanks Eric! Using version 2.12.1 has fixed the issue.