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Adapt to geposan changes and add new methods

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This commit is contained in:
Elias Projahn 2021-11-14 22:34:46 +01:00
parent 9709360d45
commit f485eadaf5
4 changed files with 61 additions and 49 deletions
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40
R/data.R
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@ -71,13 +71,23 @@ genes <- geposan::genes[, .(
methods <- list(
list(
id = "clusteriness",
name = "Clustering",
description = "Clustering of genes"
name = "Clustering (distances)",
description = "Clustering of genes (distances)"
),
list(
id = "clusteriness_positions",
name = "Clustering (positions)",
description = "Clustering of genes (positions)"
),
list(
id = "correlation",
name = "Correlation",
description = "Correlation with known genes"
name = "Correlation (distances)",
description = "Correlation with known genes (distances)"
),
list(
id = "correlation_positions",
name = "Correlation (positions)",
description = "Correlation with known genes (positions)"
),
list(
id = "proximity",
@ -91,6 +101,12 @@ methods <- list(
)
)
# IDs of methods for geposan.
method_ids <- sapply(methods, function(method) method$id)
# Names of methods for geposan.
method_names <- sapply(methods, function(method) method$name)
# Gene IDs of known or suggested TPE-OLD genes.
genes_tpe_old <- genes[suggested | verified == TRUE, id]
@ -99,17 +115,17 @@ species_replicative <- species[replicative == 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
methods = method_ids,
species_ids = species$id,
gene_ids = genes$id,
reference_gene_ids = 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_replicative,
genes = genes$id,
reference_genes = genes_tpe_old
methods = method_ids,
species_ids = species_replicative,
gene_ids = genes$id,
reference_gene_ids = genes_tpe_old
)