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Add new method adjacency

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Elias Projahn 2021-11-25 20:55:11 +01:00
parent b1eff374b3
commit 88b1a9ab6a
3 changed files with 85 additions and 6 deletions
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9
R/preset.R
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@ -11,14 +11,10 @@
#'
#' - `clusteriness` How much the gene distances to the nearest telomere
#' cluster across species.
#' - `clusteriness_positions` The same as `clusteriness` but using absolute
#' gene positions instead of distances.
#' - `correlation` The mean correlation of gene distances to the nearest
#' telomere across species.
#' - `correlation_positions` Correlation using position data.
#' - `neural` Assessment by neural network trained using distances.
#' - `neural_positions` Assessment by neural network trained using absolute
#' position data.
#' - `neural` Assessment by neural network trained on the reference genes.
#' - `adjacency` Proximity to reference genes.
#' - `proximity` Mean proximity to telomeres.
#'
#' Available optimization targets are:
@ -42,6 +38,7 @@ preset <- function(methods = c(
"clusteriness",
"correlation",
"neural",
"adjacency",
"proximity"
),
species_ids = NULL,