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Shiny_Pathway_dpmsr_v1.R
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Shiny_Pathway_dpmsr_v1.R
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#listOrganisms()
#string_species <- get_STRING_species(version=10)
# look up tax ID https://www.ncbi.nlm.nih.gov/taxonomy
#i=1
library(org.Hs.eg.db)
library(org.Mm.eg.db)
library(org.Rn.eg.db)
tax_list <- c("Human", "Mouse", "Rat")
tax_db_list <- c(org.Hs.eg.db, org.Mm.eg.db, org.Rn.eg.db)
organism_list <- c("Homo sapiens", "Mus musculus", "Rattus norvegicus")
go_list <- c("human", "mouse", "rat")
string_dir <- '/home/dpmsr/shiny_PD/'
for (i in (1:length(tax_list))){
tax_choice <- tax_list[i]
tax_db <- tax_db_list[i]
organism_choice <- organism_list[i]
go_choice <- go_list[i]
cat(file=stderr(), str_c(tax_choice, " ", organism_choice, " ", go_choice), "\n" , "\n")
wp.gmt <- rWikiPathways::downloadPathwayArchive(date = "20220110", organism=organism_choice, format = "gmt", destpath = string_dir)
wp2gene <- clusterProfiler::read.gmt(str_c(string_dir, wp.gmt))
if (version$major < 4){
wp2gene <- wp2gene %>% tidyr::separate(ont, c("name","version","wpid","org"), "%")
}else {
wp2gene <- try(wp2gene %>% tidyr::separate(term, c("name","version","wpid","org"), "%") )
}
Uniprot <- ViSEAGO::Uniprot2GO()
myGENE2GO <- ViSEAGO::annotate(go_choice, Uniprot)
save(wp2gene, file=str_c(string_dir,"Pathway_wp2gene_",tax_choice))
save(myGENE2GO, file=str_c(string_dir,"Pathway_myGENE2GO_",tax_choice))
}