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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)
}