GO enrichment Analysis for Sus Scrofa using WGCNA in R

Question

[susana.amaral.teixeira]

Does anyone know how to perform an enrichment analysis using GOenrichmentAnalysis function for sus scrofa using WGCNA in R?

[susana.amaral.teixeira]

Hi, Philipp.

I tried package anRichment, but it returns this message: Installing package into ‘C:/Users/Crohma/Documents/R/win-library/3.5’ (as ‘lib’ is unspecified) Warning in install.packages : package ‘anRichment’ is not available (for R version 3.5.1)

Then, I have trying other versions: v.3.0, v.3.4, v3.5.1, v.3.6, but I have no success too.

What do version you use to this package in R?

[h.mon]

Are you following correctly the install instructions? Can you show which commands did you issue?

[susana.amaral.teixeira]

Hi, sorry! This is no version error...but another type.

I am using this code obteined from: https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/GeneAnnotation/Tutorials/anRichment-Tutorial1.pdf

source("http://bioconductor.org/biocLite.R"); biocLite(c("AnnotationDBI", "GO.db", "org.Hs.eg.db", "org.Mm.eg.db", "XML", "WGCNA", "TxDb.Hsapiens.UCSC.hg19.knownGene", "TxDb.Mmusculus.UCSC.mm10.knownGene"));

source("http://bioconductor.org/biocLite.R"); biocLite(c("org.Ss.eg.db")); ##Sus Scrofa (Ss)

install.packages("C:\Users\Crohma\AppData\Local\Temp\RtmpSUkmE1\downloaded_packages", "anRichmentMethods", repos = NULL, type = "source") #my path

install.packages("C:\Users\Crohma\AppData\Local\Temp\RtmpSUkmE1\downloaded_packages","anRichment", repos = NULL, type = "source")

But... Warning in install.packages : 'lib = "anRichment"' is not writable Warning: invalid package 'C:/Users/Crohma/AppData/Local/Temp/RtmpSUkmE1/downloaded_packages' Erro: ERROR: no packages specified In R CMD INSTALL Warning in install.packages : installation of package ‘C:/Users/Crohma/AppData/Local/Temp/RtmpSUkmE1/downloaded_packages’ had non-zero exit status

library("anRichment"); Error in library("anRichment") : there is no package called ‘anRichment’

So, I tried step-by-step according Tutorial: source(paste0("https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork","GeneAnnotation/installAnRichment.R")); installAnRichment();

But, I have received the same error message: options(stringsAsFactors = FALSE); library("anRichment"); library("anRichment"); Error in library("anRichment") : there is no package called ‘anRichment’

[Philipp Bayer]

Are you installing this on your own computer?

lib = "anRichment"' is not writable

means that you do not have write permissions on the folder where R tries to install the package. You can re-run R as administrator to maybe to get that working.

Answer 1

[Philipp Bayer]

First of all, WGCNA is deprecated and tells you to use a different package:

 NOTE: GOenrichmentAnalysis is deprecated. Please use function enrichmentAnalysis from R package anRichment, available from https://labs.genetics.ucla.edu/horvath/htdocs/CoexpressionNetwork/GeneAnnotation/

Second, WGCNA does not support Sus scrofa, only these ones:

 "human", "mouse", "rat", "malaria", "yeast", "fly", "bovine", "worm", "canine", "zebrafish", "chicken".

This older pig paper used GOstats instead: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3453518/
This more recent paper used DAVID: https://academic.oup.com/dnaresearch/advance-article/doi/10.1093/dnares/dsz006/5476584