Convert to R package

R/data.R

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+# Species IDs of known replicatively aging species.
+species_ids_replicative <- c(
+    "bihybrid",
+    "btaurus",
+    "bthybrid",
+    "cfamiliaris",
+    "chircus",
+    "cjacchus",
+    "clfamiliaris",
+    "csabaeus",
+    "ecaballus",
+    "fcatus",
+    "ggorilla",
+    "hsapiens",
+    "lafricana",
+    "mfascicularis",
+    "mmulatta",
+    "mmurinus",
+    "mnemestrina",
+    "nleucogenys",
+    "oaries",
+    "pabelii",
+    "panubis",
+    "ppaniscus",
+    "ptroglodytes",
+    "sscrofa",
+    "tgelada"
+)
+
+# Species from [geposan] and their aging status.
+species <- geposan::species[, .(
+    id,
+    name,
+    replicative = id %chin% species_ids_replicative
+)]
+
+# Gene names of genes for verified TPE-OLD genes.
+genes_verified_tpe_old <- c(
+    "C1S",
+    "DSP",
+    "ISG15",
+    "SORBS2",
+    "TERT"
+)
+
+# Gene names of genes with a suggested TPE-OLD.
+genes_suggested_tpe_old <- c(
+    "AKAP3",
+    "ANO2",
+    "CCND2",
+    "CD163L1",
+    "CD9",
+    "FOXM1",
+    "GALNT8",
+    "NDUFA9",
+    "TEAD4",
+    "TIGAR",
+    "TSPAN9"
+)
+
+# Genes from [geposan] and their TPE-OLD status.
+genes <- geposan::genes[, .(
+    id,
+    name,
+    chromosome,
+    suggested = name %chin% genes_suggested_tpe_old,
+    verified = name %chin% genes_verified_tpe_old
+)]
+
+# All available methods from [geposan] and additional information on them.
+methods <- list(
+    list(
+        id = "clusteriness",
+        name = "Clustering",
+        description = "Clustering of genes"
+    ),
+    list(
+        id = "correlation",
+        name = "Correlation",
+        description = "Correlation with known genes"
+    ),
+    list(
+        id = "proximity",
+        name = "Proximity",
+        description = "Proximity to telomeres"
+    ),
+    list(
+        id = "neural",
+        name = "Neural",
+        description = "Assessment by neural network"
+    )
+)
+
+# Gene IDs of known or suggested TPE-OLD genes.
+genes_tpe_old <- genes[suggested | verified == TRUE, id]
+
+# Preset for [geposan] including all species and TPE-OLD genes for reference.
+preset_all_species <- geposan::preset(
+    methods = c("clusteriness", "correlation", "proximity", "neural"),
+    species = species$id,
+    genes = genes$id,
+    reference_genes = genes_tpe_old
+)
+
+# Preset for [geposan] including only replicatively aging species as well as
+# TPE-OLD genes for reference.
+preset_replicative_species <- geposan::preset(
+    methods = c("clusteriness", "correlation", "proximity", "neural"),
+    species = species_ids_replicative,
+    genes = genes$id,
+    reference_genes = genes_tpe_old
+)