genomicElementDistribution function not found
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Arunima ▴ 10
@2832c5da
Last seen 5 weeks ago
United States

Hello everyone

I tried to use the function "genomicElementDistribution" to annotate the peak location using the library ChIpeakAnno, but it says the function not found. Do you suggest me to update the library?

Thanks

Code should be placed in three backticks as shown below


# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )
ChIPpeakAnno • 115 views
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@james-w-macdonald-5106
Last seen 1 hour ago
United States

Have you already loaded the package? Also, this part of the default question

# include your problematic code here with any corresponding output 
# please also include the results of running the following in an R session 

sessionInfo( )

Is placed there to remind you that you need to include the results of running sessionInfo() in your R session, which would A). Tell us whether or not you have loaded the package, so we don't have to ask you, and B.) tell us the version of ChiPpeakAnno you are using. Which brings up the next point. The NEWS file for this package has this:

CHANGES IN VERSION 3.23.9
-------------------------

    o add new function enrichmentPlot, genomicElementDistribution, genomicElementUpSetR, and methagenePlot to improve visualization.

Which tells you when they added the function you are trying to use, and which you could have used to figure out if your version does include the function.

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Package: ChIPpeakAnno Type: Package Version: 3.0.0 Date: 2014-10-24 License: LGPL LazyLoad: yes

I have the following package installed

How do I update the package with the new version.

Thanks

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Hi Arunima,

You need to install R 4.1 first. Then, start R (version "4.1") and enter: if (!requireNamespace("BiocManager", quietly = TRUE))

install.packages("BiocManager")

BiocManager::install("ChIPpeakAnno")

Best regards,

Julie

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