load_database {cuperdec}

Load database

Description

Loads a taxon/isolation source database file, i.e. first column is a list of taxa, and the second column is a list of isolation sources, and formats for downstream analysis.

Usage

load_database(x, target)

Arguments

x

Path to a (minimum) two column TSV file or tidy dataframe (e.g. tibble), one column with taxon names and other indicating if from target isolation source.

target

the string in the 'Isolation Source' (i.e. 2nd) column which is the expected target source of the samples

Details

Taxon names should match that with the taxa table.

Value

A tibble, formatted for use in downstream cuperdec functions.

Examples

data(cuperdec_database_ex)
iso_database <- load_database(cuperdec_database_ex, target = "oral")