Description Usage Arguments Details Value Examples
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.
1 | load_database(x, target)
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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 |
Taxon names should match that with the taxa table.
A tibble, formatted for use in downstream cuperdec functions.
1 2 | data(cuperdec_database_ex)
iso_database <- load_database(cuperdec_database_ex, target = "oral")
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