From 581b120cfd5dc9e6279a56407e8e3e05b57af65a Mon Sep 17 00:00:00 2001 From: Kyle Bittinger Date: Wed, 26 Jun 2024 06:00:58 -0400 Subject: [PATCH] Extracted functions what_antibiotic and what_phenotype --- R/match.R | 23 ++++++++++++++++------- 1 file changed, 16 insertions(+), 7 deletions(-) diff --git a/R/match.R b/R/match.R index 4221235..9da308e 100644 --- a/R/match.R +++ b/R/match.R @@ -29,6 +29,12 @@ antibiotic_susceptibility <- function (lineage, antibiotic, db = mirixdb::taxon_susceptibility) { + what_antibiotic(lineage, antibiotic, db) +} + +what_antibiotic <- function (lineage, + antibiotic, + db = mirixdb::taxon_susceptibility) { is_relevant <- db$antibiotic %in% antibiotic db <- db[is_relevant, c("taxon", "rank", "value")] @@ -75,18 +81,21 @@ phenotype_susceptibility <- function (lineage, phenotype, susceptibility, db = mirixdb::taxon_phenotypes) { - is_relevant <- db[[phenotype]] %in% names(susceptibility) - db <- db[is_relevant, c("taxon", "rank", phenotype)] - # match_annotation() requires a column named "value" - colnames(db)[3] <- "value" - - phenotype_values <- match_annotation(lineage, db) - + phenotype_values <- what_phenotype(lineage, phenotype, db) susceptibility_values <- susceptibility[phenotype_values] susceptibility_values <- unname(susceptibility_values) susceptibility_values } +what_phenotype <- function (lineage, + phenotype, + db = mirixdb::taxon_phenotypes) { + db <- db[, c("taxon", "rank", phenotype)] + # match_annotation() requires a column named "value" + colnames(db)[3] <- "value" + match_annotation(lineage, db) +} + # Determine the annotation values for each lineage # # @param lineage A vector of taxonomic assignments or lineages