Add external sequences to a phyloseq object — add_external_seq

Useful to compute true negative values with functions tc_metrics_mock() and tc_metrics_mock_vec().

Note the that the tax_table for additional sequences is full of NA and that the corresponding otu_table is full of 0.

Usage

add_external_seq_pq(physeq, ext_seqs, prefix = "external_")

Arguments

physeq: (required) A phyloseq-class object obtained using the phyloseq package.
ext_seqs: (DNAStringSet, required) A DNAStringSet object containing external sequences to add.
prefix: (character, default "external_") A prefix to add to the taxa name.

Value

A phyloseq object

Author

Adrien Taudière

Examples

add_external_seq_pq(
  data_fungi_mini,
  Biostrings::readDNAStringSet(
    system.file("extdata/ex_little.fasta", package = "MiscMetabar")
  )
)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 47 taxa and 137 samples ]
#> sample_data() Sample Data:       [ 137 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 47 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 47 reference sequences ]