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Add options to configure default gene sets

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This commit is contained in:
Elias Projahn 2022-05-19 16:24:23 +02:00
parent 22f5e86625
commit 74d7865389
9 changed files with 391 additions and 370 deletions
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62
R/data.R
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@ -1,65 +1,3 @@
# 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"
)
# 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 <- geposan::all_methods()