Raw AMR files plus metadata to phyloseq object — amr_raw_to_metagenomeseq • epi2me2r

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

if (FALSE) {
amr_raw_to_phyloseq(path.to.amr.files = path/to/amr.count.table,
metadata = metadata, coveragenumber = 80, keepSNP = FALSE)
}