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)
}