mirror of
https://github.com/johrpan/geposanui.git
synced 2025-10-26 19:27:24 +01:00
125 lines
2.2 KiB
R
125 lines
2.2 KiB
R
source("clustering.R")
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source("correlation.R")
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source("input.R")
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source("neural.R")
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source("util.R")
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# Load input data
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species <- run_cached("input_species", retrieve_species)
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genes <- run_cached("input_genes", retrieve_genes)
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distances <- run_cached(
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"input_distances",
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retrieve_distances,
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species[, id],
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genes[, id]
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)
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# Load processed data
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all_species <- species[, id]
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replicative_species <- species[replicative == TRUE, id]
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all_genes <- genes[, id]
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tpe_old_genes <- genes[suggested | verified == TRUE, id]
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clustering_all <- run_cached(
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"clustering_all",
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process_clustering,
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distances,
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all_species,
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all_genes
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)
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clustering_replicative <- run_cached(
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"clustering_replicative",
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process_clustering,
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distances,
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replicative_species,
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all_genes
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)
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correlation_all <- run_cached(
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"correlation_all",
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process_correlation,
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distances,
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all_species,
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all_genes,
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tpe_old_genes
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)
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correlation_replicative <- run_cached(
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"correlation_replicative",
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process_correlation,
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distances,
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replicative_species,
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all_genes,
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tpe_old_genes
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)
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neural_all <- run_cached(
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"neural_all",
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process_neural,
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distances,
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all_species,
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all_genes,
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tpe_old_genes
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)
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neural_replicative <- run_cached(
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"neural_replicative",
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process_neural,
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distances,
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replicative_species,
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all_genes,
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tpe_old_genes
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)
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# Merge processed data as well as gene information.
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results_all <- merge(
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genes,
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clustering_all,
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by.x = "id",
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by.y = "gene"
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)
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results_all <- merge(
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results_all,
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correlation_all,
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by.x = "id",
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by.y = "gene"
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)
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results_all <- merge(
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results_all,
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neural_all,
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by.x = "id",
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by.y = "gene"
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)
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results_replicative <- merge(
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genes,
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clustering_replicative,
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by.x = "id",
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by.y = "gene"
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)
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results_replicative <- merge(
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results_replicative,
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correlation_replicative,
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by.x = "id",
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by.y = "gene"
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)
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results_replicative <- merge(
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results_replicative,
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neural_replicative,
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by.x = "id",
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by.y = "gene"
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)
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# Rename `id` columns to `gene`.
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setnames(results_all, "id", "gene")
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setnames(results_replicative, "id", "gene")
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