amr_read_taxonomy: assign taxonomy for phylogenetic and AMR for each read

In epi2me2r: Process Nanopore EPI2ME Output for Use in R

assign taxonomy for phylogenetic and AMR for each read

Description

Given raw data for AMR and WIMP, provides full AMR and taxon info for those reads that assign to both

Arguments

path.to.wimp.files	path to folder containing raw CSV files from WIMP analysis
path.to.amr.files	path to folder containing raw CSV files from ARMA analysis
coveragenumber	Minimum percentage of a gene that must be covered. Range from 0 to 99, default = 80

Value

data.frame with double classified reads

Examples

## Not run: 
amr_read_taxonomy(path.to.wimp.files = "path/to/wimp_files",
path.to.amr.files = "path/to/amr_files", coveragenumber = 80)

## End(Not run)

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