functions to get binary matrix for geno + pheno data

[katholt]

Created getBinMat to take genotype & phenotype tables (as output by genotype 'parser' and 'import_ncbi_ast' functions), and output a new data frame with binary (1/0) variables for

• phenotype for a specified drug (two columns: R, NWT)
• genetic markers relevant to a specified list of drug classes (presence/absence, one column per marker)

Added examples to readme

To do

1. add optional list of strains that were subjected to genotyping, so we can fully account for those in which no markers were detected
2. if no drug_class_list specified, determine relevant drug classes to get markers for
3. generalise to deal with multiple drugs, or all drugs present in the phenotype table

[katholt]

added option 'keep_assay_values' (default F)

if set to TRUE, the mic and disk columns for the specified antibiotic will be included in the output matrix

• currently this just assumes there are columns labelled 'mic' and/or 'disk' and adds these to the output
• this works with the output of 'import_ncbi_ast' but we will need to

1. decide whether to rename these to include the drug name (as is currently done for the 'R' and 'NWT' binary output columns, - CHANGED SO ALL COLUM HEADERS ARE GENERIC 'pheno', 'R', 'WT' with no drug name
2. try to auto-identify columns of class 'mic' or 'disk' instead, or
3. let user specify quantitative column/s to retain - DONE

[katholt]

Added parameter keep_assay_values_from=c("mic", "disk")
for users to specify which phenotype columns to retain in the output

Could be scenarios where this is actually all you want for pheno data, and don't want binary phenotype output (or don't have appropriate columns to calculate it) so should make it possible to output ONLY assay data + binary genotype

[natacha-couto]

does this now include the measurement sign?

[katholt]

hi @natacha-couto

this function doesn't currently interpret MIC or disk data into S/I/R

the input pheno_table is expected to already have a column with interpreted phenotypes, the name of this column must be specified as a parameter

[katholt]

TO DO: add option to return S/I/R values also (helpful for downstream plots/analysis including solo_ppv_stats and upset plots) - DONE

[katholt]

updated import_ncbi_ast to interpret against ecoff and report in column 'ecoff' coded as WT/NWT

should now update getBinMat to use this if available, rather than defining NWT column based on I/R vs S - DONE