From c952458363d84635a6021c47741cd19ccb3c09f1 Mon Sep 17 00:00:00 2001
From: Louis <louis.lacoste@agroparistech.fr>
Date: Mon, 13 Oct 2025 10:25:10 +0200
Subject: [PATCH] Extracting code to load Europe samples to its own script

---
 load-europe.R | 14 ++++++++++++++
 1 file changed, 14 insertions(+)
 create mode 100644 load-europe.R

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")