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Update hAMRonization_function_v3.R #27

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Update hAMRonization_function_v3.R #27

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16 changes: 15 additions & 1 deletion R/hAMRonization_function_v3.R
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Original file line number Diff line number Diff line change
Expand Up @@ -76,6 +76,20 @@ harmonize_data <- function(user_software_name,
# convert output to data frame
py_run_string("hamronized_output_df = pandas.DataFrame(hamronized_output)")

# convert output to AMRgen genotype data frame format
hamronized_data <- py$hamronized_output_df %>%
mutate(Sample_ID = input_sequence_id) %>%
mutate(marker = as.gene(gene_symbol)) %>%
mutate(drug_agent = antimicrobial_agent) %>%
select(Sample_ID, marker, drug_class, drug_agent)

# Separate drug classes for rgi data
if (user_software_name=="rgi"){
hamronized_data <- hamronized_data %>%
separate_longer_delim(., drug_class, delim=";") %>%
mutate(drug_class = str_trim(drug_class, side = "both"))
}

# return harmonized data frame
return(py$hamronized_output_df)
return(hamronized_data)
}
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