From d012a1cf4d2908c7d2418be06fea587ef8d54568 Mon Sep 17 00:00:00 2001 From: Kat Holt <drkatholt@gmail.com> Date: Sat, 25 Jan 2025 09:34:04 +0000 Subject: [PATCH] Update README.md --- README.md | 14 +++++++------- 1 file changed, 7 insertions(+), 7 deletions(-) diff --git a/README.md b/README.md index 8e95af1..d1206c1 100644 --- a/README.md +++ b/README.md @@ -96,20 +96,20 @@ optionally: - `MIC (mg/L)` -> as.mic -> new column 'mic' (class mic) - `Disk diffusion (mm)` -> as.disk -> new column 'disk' (class disk) - `Testing standard` -> new column 'guideline' (character; value = 'CLSI' if specified, otherwise default to 'EUCAST') -- optionally (on by default), interpret any mic or disk columns using the ab, mo, guideline values - new column 'pheno' (class sir) +- optionally (off by default), interpret any mic or disk columns using the ab, mo, guideline values - new column 'pheno' (class sir) - return = dataframe with the input NCBI AST file contents with the new columns added ### Expected workflow (target for dev) -* import genotype data -> genotype dataframe +* import genotype data -> genotype dataframe (e.g. `parse_amrfp`) * import phenotype data -> phenotype dataframe (e.g. `import_ncbi_ast`) - interpret SIR if required (as.sir; requires either a species column, or that all rows are a single species) -* filter both files to the required sample sets (e.g. filter on species, check common sample identifiers exist) +* optionally: filter both files to the desired sample sets (e.g. filter on species, check common sample identifiers exist) * pass filtered genotype & phenotype objects (which have common sample identifiers) to functions for - - cross-tabulating SIR vs marker presence/absence, calculating & plotting PPV - - upset plots showing MIC/DD distribution stratified by genotype profile - - generating binary matrix of SIR vs marker presence/absence suitable for regression modelling - - + - generating binary matrix of SIR vs marker presence/absence suitable for regression modelling (`getBinMat`) + - cross-tabulating SIR vs marker presence/absence, calculating & plotting PPV (`solo_ppv_analysis`) + - upset plots showing MIC/DD distribution stratified by genotype profile (`AMRGen_Upset`) + # Working examples ```