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Update README.md
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katholt authored Jan 31, 2025
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Expand Up @@ -93,7 +93,7 @@ soloPPV_cipro <- solo_ppv_analysis(geno, pheno, antibiotic="Ciprofloxacin", drug
soloPPV_cipro$solo_stats
# plot PPV summary:
soloPPV_cipro$combinedplot
soloPPV_cipro$combined_plot
# get matrix combining data on ciprofloxacin phenotype (MIC, plus binary R and NWT) and genotype (binary presence/absence for quinolone resistance markers)
cip_bin<- get_binary_matrix(geno, pheno, antibiotic="Ciprofloxacin", drug_class_list=c("Quinolones"), sir_col="Resistance phenotype", keep_assay_values=T, keep_assay_values_from = "mic")
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