jrosados/CNR_IC50_MIPs

This repository contains R scripts and raw data used for the article: – “Ex vivo susceptibility to antimalarial drugs and polymorphisms in drug resistance genes of African Plasmodium falciparum, 2016-2023: a genotype-phenotype association study” # CNR_IC50_MIPs This repository contains R scripts and raw data used for the article: **"Assessment of ex-vivo antimalarial drug efficacy in African *Plasmodium falciparum* parasite isolates, 2016-2023: a genotype-phenotype association study"** The IC50 Data is contained in the *"raw_data"* folder: "CNR_epi.csv", "Countries_rank.csv" and "CNR_IC50_epidata.csv" contain IC50 data and epidemiological data from isolates. The genotype data is contained in the *"raw_data"* folder: "alternate_AA_table.csv", "coverage_AA_table.csv", "reference_AA_table.csv", "barcode_counts.csv" and "all_haplotypes.csv" files were extracted using **MIPtools** and **miplicorn** . COI_calls.csv file was generated using R package RealMcCoil(v.1.3.1). For more details on MIPs for Drug Resistance see . # R markdown files (.Rmd) contain scripts to perform the following analysis: # 1.- Data processing from MIP to csv databases 1.1 - Data processing from MIP wrangling to csv databases 1.2 - Merging genotype database with IC50 database and COI data 1.2 - Coverage heatmap 1.3 - COI distribution 1.4 - Parasitemia distribution # 2.- Epidemiological data 2.1 - Epitable 2.2 - Geographical distribution of samples # 3.- Half-maximal inhibitory concentration IC50 3.1.- Drug correlation matrix 3.2.- Drug susceptibility by year 3.3.- Distribution of resistant isolates 3.4.- Drug susceptibility by African region # 4- Validated_mutations 4.1.- Prevalence of validated key mutations 4.2.- Prevalence of k13 mutations 4.3.- Prevalence of background and other mutations 4.4.- Raw data table per year 4.5.- Raw data table in the top countries 4.6.- Temporal change of key resistance mutations by year 4.7.- Prevalence of key resistance mutations by year and by country # 5.- Proportion_mixed_pure_genotypes 5.1.- Proportion of mixed infections in key mutations 5.2.- Proportion of mixed infections in k13 gene # 6.- Haplotypes 6.1.- CRT haplotypes 6.2.- DHFR haplotypes 6.3.- DHPS haplotypes 6.4.- DHPS-DHFR haplot …