Correlate phenotype and genotype - compare AMR gene classes with resistance phenotypes from Olga's spreadsheets

[hollygene]

• [x] Subset genoype data into AMR-detected, no AMR detected
• [x] Group samples with same AMR genes

[hollygene]

^ above tasks are not appropriate for the dataset

Instead:

• [x] Subset genotype data into individual antibiotic classes (there are 16)
• [x] Determine the appropriate class for each antibiotic tested in phenotypic data
• [x] Bin antibiotics in phenotypic data into each antibiotic class from genotypic data
• [x] Correlate genotype + phenotype per antibiotic class

[hollygene]

	Phenotype: Susceptible		Phenotype: Resistant
Class	Genotype: S	Genotype: R	Genotype: S	Genotype: R	match	total	correlation
AMINOGLYCOSIDE	1058	180	30	18	1076	1286	83.6702955
Amikacin	492	96	3	0	492	591	83.248731

[hollygene]

Phenotype: Susceptible		Phenotype: Resistant
Genotype: R	Genotype: S	Genotype: R	Genotype: S
6	14	2	14
6	9	0	7