diff --git a/load-europe.R b/load-europe.R new file mode 100644 index 0000000..274e6b1 --- /dev/null +++ b/load-europe.R @@ -0,0 +1,14 @@ +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")