GO enrichment Analysis for Sus Scrofa using WGCNA in R
Does anyone know how to perform an enrichment analysis using GOenrichmentAnalysis function for sus scrofa using WGCNA in R?
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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
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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?
Are you following correctly the install instructions? Can you show which commands did you issue?
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
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’
Are you installing this on your own computer?
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.