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63 lines
No EOL
1.6 KiB
R
63 lines
No EOL
1.6 KiB
R
source("clusteriness.R")
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source("correlation.R")
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source("neural.R")
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source("proximity.R")
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#' Construct a new method.
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#'
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#' A method describes a way to perform a computation on gene distance data that
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#' results in a single score per gene. The function should accept the following
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#' parameters in this order:
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#'
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#' - `distances` Distance data to use.
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#' - `species_ids` Species, whose data should be included.
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#' - `gene_ids` Genes to process.
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#' - `reference_gene_ids` Genes to compare to.
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#'
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#' The function should return a `data.table` with the following columns:
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#'
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#' - `gene` Gene ID of the processed gene.
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#' - `score` Score for the gene between 0.0 and 1.0.
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#'
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#' @param id Internal identifier for the method.
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#' @param name Human readable name for the method.
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#' @param description Short human readable description.
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#' @param fn Function to perform the computation.
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#'
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#' @return A named list containing the arguments.
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method <- function(id, name, description, fn) {
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list(
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id = id,
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name = name,
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description = description,
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fn = fn
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)
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}
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#' All methods to be included in the analysis.
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methods <- list(
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method(
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"clusteriness",
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"Clustering",
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"Clustering of genes",
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process_clusteriness
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),
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method(
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"correlation",
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"Correlation",
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"Correlation with known genes",
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process_correlation
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),
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method(
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"proximity",
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"Proximity",
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"Proximity to telomeres",
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process_proximity
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),
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method(
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"neural",
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"Neural",
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"Assessment by neural network",
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process_neural
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)
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) |