polarolouis/human-microbiome-compendium
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base: polarolouis:d618e1b5d763a45e555b9074d3911b6c518feb62
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polarolouis:main
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compare: polarolouis:a8bdeecb3a468e80e41c2caaf649621c60c1cbca
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polarolouis:main

2 commits
d618e1b5d7 ... a8bdeecb3a

Author SHA1 Message Date
Louis
a8bdeecb3a fix save path 2026-02-23 14:07:18 +01:00
Louis
4d5415bbf4 fix 2026-02-23 14:05:52 +01:00
2 changed files with 5 additions and 1 deletions
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4
blockmodels_correct_sampling_effort.R
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@ -26,6 +26,10 @@ message("At level: ", level, " starting at: ", epoch)
save_path <- here("results", "seq-effort", paste0(author, "_", level, "_", epoch, ".Rds")) save_path <- here("results", "seq-effort", paste0(author, "_", level, "_", epoch, ".Rds"))
if (!dir.exists(save_path)) {
dir.create(save_path, recursive = TRUE)
}
per_taxa_networks <- collapse_otu_at_taxo(the_data) per_taxa_networks <- collapse_otu_at_taxo(the_data)
covar_mat <- t(colSums(per_taxa_networks[[level]]) %*% t(rep(1, nrow(per_taxa_networks[[level]])))) covar_mat <- t(colSums(per_taxa_networks[[level]]) %*% t(rep(1, nrow(per_taxa_networks[[level]]))))

2
sge_scripts/bm_correct_sampling.sh
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@ -45,4 +45,4 @@ readonly NB_CORES=$(sed -n 's/^#\$ -pe thread \(.*\)/\1/p' -- "$0")
echo -n "Model will be $MODE with $NB_CORES" echo -n "Model will be $MODE with $NB_CORES"
Rscript "${APPLICATIONS_DIR}/blockmodels_correct_sampling_effort.R.R" $MODE &>> logs/$JOB_NAME.$SGE_TASK_ID Rscript "${APPLICATIONS_DIR}/blockmodels_correct_sampling_effort.R" $MODE &>> logs/$JOB_NAME.$SGE_TASK_ID