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Properly access distance data

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This commit is contained in:
Elias Projahn 2021-10-21 14:26:03 +02:00
parent c0a1d965d7
commit 21a5817988
5 changed files with 12 additions and 18 deletions
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R/correlation.R
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@ -1,12 +1,12 @@
# Compute the mean correlation coefficient comparing gene distances with a set
# of reference genes.
correlation <- function(distances, preset, progress = NULL) {
correlation <- function(preset, progress = NULL) {
species_ids <- preset$species_ids
gene_ids <- preset$gene_ids
reference_gene_ids <- preset$reference_gene_ids
# Prefilter distances by species.
distances <- distances[species %chin% species_ids]
distances <- geposan::distances[species %chin% species_ids]
# Tranform data to get species as rows and genes as columns. We construct
# columns per species, because it requires fewer iterations, and transpose