amr_raw_to_metagenomeseq: 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. metagenomeSeq package required.

Arguments

path.to.amr.files	path to folder containing raw CSV files from ARMA CARD analysis
metadata	data.table of metadata with "filename" and "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

metagenomeSeq object for downstream analysis

See Also

metagenomeSeq

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.