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Perform file existence check in load script

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Louis 2025-10-13 13:41:05 +02:00
parent ad91ae0ef1
commit 5cf922d69f
1 changed files with 17 additions and 13 deletions
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30
load-europe.R
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@ -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")
}