'RInterpreterError: Failed to parse and evaluate line when running R code on Google Colab
I want to run an R code on Google Colaboratory to generate hsa.txt file.
First cell:
%load_ext rpy2.ipython
Second cell:
%%R
install.packages("BiocManager")
BiocManager::install("KEGGREST")
BiocManager::install("EnrichmentBrowser")
library(KEGGREST)
library(EnrichmentBrowser)
library(org.Hs.eg.db)
MRSA252 <- keggList("hsa")
sarpathway <- downloadPathways("hsa")
hsa <- getGenesets(org="hsa", db="kegg", cache=TRUE, return.type="list")
for (i in 1:length(hsa)) {
t <- unlist(mget(hsa[[i]], envir=org.Hs.egSYMBOL, ifnotfound=NA),use.names=FALSE)
hsa[[i]] <- t[!is.na(t)]
# Remove disease-specific pathways
hsa[[i]] <- hsa[!grep("disease$", hsa)]
}
writeGMT(hsa, gmt.file="hsa.txt")
Traceback:
RInterpreterError: Failed to parse and evaluate line '\ninstall.packages("BiocManager")\nBiocManager::install("KEGGREST")\nBiocManager::install("EnrichmentBrowser")\n\nlibrary(KEGGREST)\nlibrary(EnrichmentBrowser)\nlibrary(org.Hs.eg.db)\n\nMRSA252 <- keggList("hsa")\nsarpathway <- downloadPathways("hsa")\n\n\n\nhsa <- getGenesets(org="hsa", db="kegg", cache=TRUE, return.type="list")\nfor (i in 1:length(hsa)) {\n t <- unlist(mget(hsa[[i]], envir=org.Hs.egSYMBOL, ifnotfound=NA),use.names=FALSE)\n hsa[[i]] <- t[!is.na(t)]\n # Remove disease-specific pathways\n hsa[[i]] <- hsa[!grep("disease$", hsa)]\n}\nwriteGMT(hsa, gmt.file="hsa.txt")'.
R error message: 'Error in .getUrl(url, .textParser) : Forbidden (HTTP 403).'
Sources
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Source: Stack Overflow
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