19 lines
659 B
R
19 lines
659 B
R
library(MicroBioMap)
|
|
library(phyloseq)
|
|
library(mia)
|
|
|
|
if (!(file.exists("data/hmc-phyloseq-europe.Rds") || file.exists("data/hmc-phyloseq.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)
|
|
saveRDS(cpd_phyloseq, "data/hmc-phyloseq.Rds")
|
|
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")
|
|
}
|