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Convert raw AMR CSV files to data table

Arguments

path.to.amr.files

path to folder containing raw CSV files from ARMA CARD analysis

coveragenumber

Minimum percentage of a gene that must be covered. Range from 0 to 99, default = 80

keepSNP

TRUE or FALSE: whether to keep AMR gene conferred by one SNP change, default = FALSE

Value

data.table of AMR genes at a specific coverage with or without SNP associated

Examples

if (FALSE) {
read_in_amr_files(path.to.amr.files = "~/Desktop/my.files/",
coveragenumber = 80, keepSNP = FALSE)
}