diff --git a/load-europe.R b/load-europe.R index 274e6b1..d722661 100644 --- a/load-europe.R +++ b/load-europe.R @@ -1,14 +1,18 @@ -library(MicroBioMap) -library(phyloseq) -library(mia) +if (!file.exists("data/hmc-phyloseq-europe.Rds")) { + library(MicroBioMap) + library(phyloseq) + library(mia) -cpd <- getCompendium() -cpd_phyloseq <- convertToPhyloseq(x = cpd) -sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe") -rm(cpd) -gc() -sample_data(cpd_phyloseq) -cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name)) -rm(cpd_phyloseq) -gc() -saveRDS(cpd_phyloseq_europe, "data/hmc-phyloseq-europe.Rds") + cpd <- getCompendium() + cpd_phyloseq <- convertToPhyloseq(x = cpd) + sample_data(cpd_phyloseq)$geo_loc_name |> grepl(pattern = "europe") + rm(cpd) + gc() + sample_data(cpd_phyloseq) + cpd_phyloseq_europe <- subset_samples(cpd_phyloseq, grepl("europe", geo_loc_name)) + rm(cpd_phyloseq) + gc() + saveRDS(cpd_phyloseq_europe, "data/hmc-phyloseq-europe.Rds") +} else { + cpd_phyloseq_europe <- readRDS("data/hmc-phyloseq-europe.Rds") +}