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Reorganize source files and generalize presets

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This commit is contained in:
Elias Projahn 2021-10-16 21:46:59 +02:00
parent 8104e9bd8a
commit 68354bf808
14 changed files with 119 additions and 147 deletions
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29
process/presets.R Normal file
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library(data.table)
#' Create a new preset.
#'
#' A preset is a combination of input values to all processing methods. The
#' preset's hash will be used to cache the results of applying those.
#'
#' @param species_ids IDs of species to include.
#' @param reference_gene_ids Reference genes to use.
#'
#' @return A named list containing the arguments.
preset <- function(species_ids, reference_gene_ids) {
list(
species_ids = species_ids,
reference_gene_ids = reference_gene_ids
)
}
#' A default preset including only replicatively aging species.
preset_replicative_species <- preset(
species[replicative == TRUE, id],
genes[suggested | verified == TRUE, id]
)
#' A default preset including all species.
preset_all_species <- preset(
species[, id],
genes[suggested | verified == TRUE, id]
)