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Extracting code to load Europe samples to its own script

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Louis 2025-10-13 10:25:10 +02:00
parent 8bbfec9e49
commit c952458363
1 changed files with 14 additions and 0 deletions
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load-europe.R Normal file
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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")