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r-packages's Introduction

R-packages

All the R packages created in Hidelab

  1. pathprint, version 1.4.0, uploaded 22/09/2017
  2. pathprintGEOData, version 1.2.0, uploaded 22/09/2017
  3. pcxn, 1.1.0, uploaded 3/11/2017
  4. pcxnData, 1.0.0, uploaded 3/11/2017

Future work

  1. Update the pcxnData package on Bioconductor with 4 new unadjsuted correlation matrices and update the geneset matrix by adding ADCL
  2. Update the pcxn package on Bioconductor by adding the unadjusted parameter in the explore and analyze functions, which will utilize the new pcxnData package

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r-packages's Issues

Cannot load pcxn

install.packages("pcxn_0.99.0.tar.gz")
inferring 'repos = NULL' from 'pkgs'

  • installing source package ‘pcxn’ ...
    ** R
    ** data
    *** moving datasets to lazyload DB
    ** inst
    ** preparing package for lazy loading
    ** help
    *** installing help indices
    ** building package indices
    ** installing vignettes
    ** testing if installed package can be loaded
  • DONE (pcxn)

library(pcxn)
Error in FUN(X[[i]], ...) :
cannot open file '/Library/Frameworks/R.framework/Versions/3.4/Resources/library/pcxn.db/data/Rdata.rdb': No such file or directory
In addition: Warning message:
In FUN(X[[i]], ...) : restarting interrupted promise evaluation

pcxn gene members error

To retrieve the genes from a geneset, I used the function - pcxn.gene_members("Alzheimer's disease (KEGG)")

which gives the following error - Error in attachNamespace("org.Hs.eg.db") : namespace is already attached

This is resolved if I unload the namespace by - unloadNamespace("org.Hs.eg.db")

Is this by design or a bug?

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