amr_raw_to_phyloseq: Raw AMR files plus metadata to phyloseq object

In epi2me2r: Process Nanopore EPI2ME Output for Use in R

Raw AMR files plus metadata to phyloseq object

Description

given directory and metadata make phyloseq object phyloseq package required.

Arguments

path.to.amr.files	path to data of raw csv files from ARMA CARD analysis
metdata	data.table of metadata with "arma_filename" and "arma_barcode" columns required
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

phyloseq object for downstream analysis

See Also

phyloseq

Examples

## Not run: 
amr_raw_to_phyloseq(path.to.amr.files = path/to/amr.count.table,
metadata = metadata, coveragenumber = 80, keepSNP = FALSE)

## End(Not run)

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