18 lines
574 B
R
18 lines
574 B
R
if (!file.exists("data/hmc-phyloseq-europe.Rds")) {
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library(MicroBioMap)
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library(phyloseq)
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library(mia)
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cpd <- getCompendium()
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cpd_phyloseq <- convertToPhyloseq(x = cpd)
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sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe")
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rm(cpd)
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gc()
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sample_data(cpd_phyloseq)
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cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name))
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rm(cpd_phyloseq)
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gc()
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saveRDS(cpd_phyloseq_europe, "data/hmc-phyloseq-europe.Rds")
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} else {
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cpd_phyloseq_europe <- readRDS("data/hmc-phyloseq-europe.Rds")
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}
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