Select columns from tax_table in a phyloseq object

Select tax_table columns (taxonomic ranks) using tidyselect semantics.

Usage

select_taxa_pq(physeq, ...)

Arguments

physeq: (phyloseq, required) A phyloseq object.
...: One or more unquoted expressions separated by commas. Variable names can be used as if they were positions in the data frame, so expressions like Phylum:Genus can be used to select a range of taxonomic ranks.

Value

A phyloseq object with selected tax_table columns.

Author

Adrien Taudière

Examples

library(MiscMetabar)
# Select specific ranks
select_taxa_pq(data_fungi, Phylum, Class)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 2 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]

# Select a range of ranks
select_taxa_pq(data_fungi, Phylum:Genus)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 5 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]

# Exclude ranks
select_taxa_pq(data_fungi, !Species)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 7 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 11 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]