read_in_amr_files: Convert raw AMR CSV files to data table

In epi2me2r: Process Nanopore EPI2ME Output for Use in R

Convert raw AMR CSV files to data table

Description

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

## Not run: 
read_in_amr_files(path.to.amr.files = "~/Desktop/my.files/",
coveragenumber = 80, keepSNP = FALSE)

## End(Not run)

epi2me2r documentation built on June 3, 2022, 9:07 a.m.