Select columns from sample_data in a phyloseq object

Select sample_data columns using tidyselect semantics.

Usage

select_samdata_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 x:y can be used to select a range of variables.

Value

A phyloseq object with selected sample_data columns.

Author

Adrien Taudière

Examples

library(MiscMetabar)
# Select specific columns
select_samdata_pq(data_fungi, Height, Time)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 2 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]

# Select a range of columns
select_samdata_pq(data_fungi, Height:Time)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 3 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]

# Exclude columns
select_samdata_pq(data_fungi, !Sample_id)
#> phyloseq-class experiment-level object
#> otu_table()   OTU Table:         [ 1420 taxa and 185 samples ]
#> sample_data() Sample Data:       [ 185 samples by 6 sample variables ]
#> tax_table()   Taxonomy Table:    [ 1420 taxa by 12 taxonomic ranks ]
#> refseq()      DNAStringSet:      [ 1420 reference sequences ]