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